Enlarge/Reduce

By casting the Reduce of Enlarge/Reduce, you will be able to do the following:

The target's size is halved in all dimensions, and its weight is reduced to one-eighth of normal.

Should you target the sails, that should hobble the ship enough to prevent movement, but also still make it easy for you to undo the effect and have a fully functioning ship.

Reducing the sails

This would likely cause the sails to fall as they no longer fit their rigging. Enlarging them again (or waiting the 1 minute for the spell to end), would just require the sailors to re-rig their ship. That's much more manageable from a simulationist perspective.

Conjure Woodland Beings + Longstrider

Problem 1: Range
If you want to catch a ship, you need to be on a faster ship. At least, that's going to be your problem with spells like Control Water. You need to get within 300 ft. Line of sight on the open ocean depends on ship height, but let's just say it's 12 miles on a 100-ft crow's nest on a clear day. You're never getting close to a faster ship that doesn't want to get caught!

Problem 2: Duration
It's not enough to stun the ship. In fact, there's no such thing as stunning a ship. It's a bobbing bit of wood in the water whose crew rigged it so that the wind and currents tend to send it in a certain direction. Lots of spells can render a crew temporarily disabled or permanently dead, but the ship will keep sailing. For an extreme example of something in this vein, read about the Mary Celeste.

Even if you halt a ship with magic, that ship is halted only as long as the magic lasts. I believe Control Water should be able to halt a ship, but it only lasts 10 minutes. I assume you're stopping this ship so that another ship can board it. How far away is that other ship, again?

Incidentally and on the subject of duration, Gust of Wind has a duration of 1 minute. I'll assume that the players' ship either can maintain Gust of Wind for hours on end or has a high speed without Gust of Wind. Otherwise, a fast ship could overtake it without the use of magic.

The math of catching a ship

You need something that can outrun the players' ship and cut its sails. That slows them dramatically until they complete a doable but time-consuming repair. It also gives them an opportunity to use the Mending spell if anyone bothered to take it.

I've seen 5-8 knots listed as a typical speed for 19th century sailing vessels. 8 knots is 13.5 ft/s or 81 ft/round. Sprites with Longstrider have a fly speed of 50, so they can fly 100 ft/round by taking the Dash action. Quicklings have a walk speed of 120 ft, so with Water Walk and Longstrider, they can dash 260 ft across water per round.

Bottom line: even with the magical wind, it's a fast ship that can outrun Sprites with Longstrider, and Quicklings with Longstrider and Water Walk are even faster.

Note that this solution does require DM cooperation. Conjure Woodland Beings lets the caster pick a CR, and the DM picks X number of creature of that CR or lower to show up. The caster can ask for a particular creature or mix of creatures, but the DM has the final say on what creatures actually show up. My best guess is that a DM is meant to be generous about granting player requests, right up until the DM feels like it would make the game stupid (repeatedly conjuring Pixies to turn the whole party into Tyranosaurus Rexes is the classic example). As I understand it, though, you ARE the DM, so that's not a problem in this situation.

Example Encounter

Here's an example of what a level 8+ druid might do when his ship catches sight of your party's ship:

• Use Conjure Woodland Beings to summon 8 Sprites.


• Cast Longstrider on the Sprites (Longstrider doesn't require concentration, so you can do this).


• Instruct the Sprites to turn invisible, fly into the target
  ship's rigging, and start cutting ropes.


• Cast Animal Messenger on a seabird with fly speed 50. Send a message
  to the target ship along the lines of "You will lay down arms and
  surrender your vessel to [insert jurisdiction]."


• Cast Water Breathing on self as a safety measure


• Jump overboard; Wildshape into a Giant Octopus and give chase, but hiding underwater


• When the sprites start destroying the rigging and the bird delivers its message, break the ship's rudder from underwater

The sprites will reappear the moment they start cutting ropes, and the ship's crew will kill them quickly thereafter. That's okay. Four cuts per mast should be plenty to cripple the ship's propulsion until the crew take the time to reset a bunch of stuff, and in the meantime your pursuing ship catches up.

If the players' ship puts up a fight when your ship catches up, remember that you're a giant octopus. Start dragging people overboard. This is particularly cruel, as there's no save against it. Every hit by a giant octopus is an automatic grapple. After a hit, all you have to do is move (rotate) so the victim is over the edge, and let them go.

Alternative

The example above is highly aggressive. If you want to build more tension, send only the sprites, then wait for your NPC's ship to catch up. "The rigging on your ship starts collapsing as sprites appear, cutting lines. You see a ship in the distance, slowly gaining on you."

Also, maybe you decide your druid doesn't have a ship, or maybe the players' ship is too fast for sprites to catch up within Conjure Woodland Beings' 1-hour duration. A level 8+ druid can get right on top of the players' ship by Wildshaping into a bird (I believe Giant Eagle with Longstrider is your fastest option), dropping into the water (with water breathing already on), and casting spells from underwater.

Control Water

This spell affects a 100' cube of water. Either redirect flow to counter the effect of the winds and hold the ship in place with currents, or part water to ground the ship or at least put it at the bottom of a 100' hole in the water.

Depending on how you want to approach it, hypnotic pattern could do the job. If enough crew members fail their save they will just be standing around doing nothing for a minute. Use that time to move in and tie them up.

Another option might be Otiluke's resilient sphere. Drop that around either the helm so they can't steer away, or whatever they use to raise the anchor.

If the crew on the ship aren't paying attention you might be able to block the ship with a few well placed floating discs. Cast enough of them under the sides of ship to support it's total weight just as the tide is about to go out. As soon as the water level has dropped enough the ship will no longer be in the water and thus be unable to sail away. You could also combo this with greater invisibility so that the caster isn't visible while they work.

Polymorph might work.

The caster could use Polymorph to turn himself or a minion of sufficient CR/level into a Giant Shark or Giant Crocodile. These are Huge beasts with swim speeds and high Strength scores. The polymorphed person could then Grapple the ship, effectively stopping it. If the Grapple was initiated beneath the surface of the water, it would be difficult for the PCs to target the polymorphed person for an attack. It might take some time for the PCs to even realize what had caused the ship to stop. They might think they had hit a reef instead of been grappled by a Huge creature, for example. The Polymorph spell requires concentration but lasts for a whole hour, which would make it effective as a stalling tactic.

If you decide Grappling a ship is not allowed (refer to @NautArch's comment), look at the Unearthed Arcana for Ships and the Sea, and use the Crashing rules.

If a ship moves into the space occupied by a creature or object, it might crash. A ship avoids crashing if the creature or object is at least two sizes smaller than it. When a ship crashes, it must immediately make a DC 10 Constitution saving throw. On a failed save, it takes damage to its hull based on the size of the creature or object it crashed into, as shown on the Crash Damage table. It also stops moving if the object or creature is bigger than it or one size smaller.

A Huge creature such as a Giant Crocodile or Giant Shark will always be at most 1 size smaller than a ship, which is Gargantuan at most. By repeatedly moving in front of the ship, the polymorphed person can force the ship to repeat saving throws until it crashes. The ship will then be forced to stop because a Huge creature is at most 1 size smaller than a ship.

Quaal's Anchor Feather Token

I'm aware that you are looking for a spell and the other answers have looked at spells in considerable depth. However, there is a particular magic item which performs precisely the task you want and I feel this question would be incomplete if I did not mention it.

Quaal's Feather Token (DMG p. 188)

Wondrous item, rare

Anchor. You can use an action to touch the token to a boat or ship. For the next 24 hours, the vessel can't be moved by any means. Touching the token to the vessel again ends the effect. When the effect ends, the token disappears.

Quaal's feather tokens appear on Magic Item Table C (DMG p. 145), which also contains 4th and 5th level spell scrolls, so by that metric it is roughly on par with 4th level spells. Additionally, Magic Item Table C is a valid treasure hoard result for monsters of CR 0-4 (DMG p. 137), so it is well within the means of an 8th level character to possess a feather token.

Depending on the abundance of magic items in your setting, if this is an NPC tasked by a port to chase down pirates it would make perfect sense for them to have magic items which would specifically help in that task. It may even be that the port authority has wizards or artificers who make anchor feather tokens, because being able to prevent a ship from disembarking would be something that is very useful for a port authority.

There are three advantages of the feather token. It has a duration of up to 24 hours (or until someone uses the token to reverse the effect) and does not require concentration, which is better than any spell. It completely blocks movement of the ship and does not damage the ship, unlike some spells which only inhibit the movement of the ship or which risk sinking the ship. And it can be used by anyone, not just a mid-level spellcaster (who would be rather expensive for the port to hire).

There are two disadvantages here, though. One is that the token has a range of touch. This means that the NPC (or their lackeys) need to get close enough to the ship to touch it. However, a bird animal companion should be able to use a feather token, so this is not too difficult to achieve. The other downside is that a consumable rare magic item may be considered to have a value greater than 100 gp (the very crude metrics in DMG p. 135 suggest its value is between 250 gp and 2500 gp; I would lean towards the lower end of this range for feather tokens). However, if your port authority really wants to stop these 'pirates', then they would be willing to spend some extra cash to get the job done properly.

With an 8th level wizard¹, Fabricate solves the problem

Turn the sails into fishnets, or into macrame hammocks. The ship goes nowhere. If there is a question as to whether or not canvas can be made into net, that's where the macrame comes in. It's cloth (well, yarn/thread) which is what sails / canvas are made from as a raw material. The trick is to stay within range (120 ') for the whole casting time.

Fabricate

Casting Time: 10 minutes / Range: 120 feet /

You convert raw materials into products of the same material. For example, you can fabricate a wooden bridge from a clump of trees, a rope from a patch
of hemp, and clothes from flax or wool. Choose raw materials that you
can see within range. {snip} The quality of objects made by the spell is commensurate with the quality of the raw materials.

Nets don't hold wind.

Once you have the ship, you can change them back in to sails.

No damage done, and Bob's your uncle.

¹ Or a Bard with magical secrets, or using a couple of scrolls, or a scroll and a ring of spell storing ...

The real stoppers come only at 5+ level, so let's start with looking at them. Oh, slight note: most of these cost little to nothing in components.

Wall of Force - 5

If it is just to stop the ship here and there, creating a magic reef in the shape of a Wall of force will stop the ship in their tracks within moments. Granted, the ship will be a wreck afterward and sink if you hit it below the shoreline.

That is unless you are smart and place the wall of force about 4 feet over the main deck in the way of the ship and cap away the masts, knock over all sailors on deck and destroy the steering without sinking the ship. Well, 120 feet range means we need some way to get someone into range.

Disintegrate - 6

A ship is huge, but if it has a 10-foot hole in the bow, it will start to leak and sink, no longer moving forward. But if you aim for the masts, it will just slow down and halt. And be a sitting duck. The problem is, you need to get within 60 feet - that's even more limited than demasting with a Wall of Force.

Ok, we got the two big showstoppers out, so, let's get creative and try to destroy the sails and stop the ship that way with good old combat magic. Sails might not come cheap, but they are huge targets, easy to hit and easy to replace - heck, most ships have smaller replacement sails that are to be used in case the sails are lost in a storm.

Produce Flame - Cantrip

Producing a small flame at touch doesn't seem dangerous to a ship, right? Well, what if we get that flame to the sails? Then they are gone, the ship will slow. A magic talent that knows Produce Flame is not that hard to come by... so we can probably find a Goblin or Kobold talent that has the spell, strap them into a glider and use a catapult to accelerate them out to the ship. With the right aiming they get there, torch the sails and probably the ship, stopping them until the rest of the fleet arrives!

Fire Bolt - Cantrip

Having to hit the sails with our mages is too hard? Well, how about having them use Fire Bolt instead?

Scorching Ray - 2

Not enough? Use Scorching Ray!

Fireball - 3

Or up it to the classic fireball.

Call Lightning - 3

Do you know how scary lightning is for a ship? Especially if it is not accompanied by rain? Once we get a caster into range, the stormcloud's lightning can and will destroy the mast and cripple it, maybe even kill the crew.

Wind Wall - 3

Well, how about we look at the walls again? There's a wall of wind, and it is surprisingly low level. It is a very strong wind... well, just enough to slow the vessel due to the mass. But it will throw down the crew which will considerably slow the ship...

Wall of Fire - 4

Or occupy the whole crew firefighting and set the sails and mast aflame the same time with a wall of fire.

Ice Storm - 4

Or shoot at the sails with icy meteors from 300 feet away. That's really tempting...

Fabricate - 4

What are sails if not huge masses of clothes that want to be made? Use Fabricate and turn the propulsion of the enemy ship into rags and dresses, or into a fishing net ... if you get someone on board of the fleeing ship for 10 minutes.

How to get the caster there?

Well, we would need either a faster ship... or use the weather or night. Or the caster needs to fly. What did I suggest up there? Oh! Strap a glider to a kobold and use a siege engine as a starter? We'd shoot the caster several hundred feet forward per round... and probably give them a flight time of 3+ turns. That makes, even if we use a humble ballista, a range of something like 0.2 miles or more - extended range upon the spell's range that is! Then add a couple gust of wind, till the caster is in range of a dimensional door (500 feet) to land on the deck... it's not hard, just bring in the naval airwings... Or get a shark to ride for the caster to cling to till he is in range.

Why not Moby Dick it:

9th level Druid of the Moon:

Wildshape into a Killer Whale (Huge)... have one of your underlings cast Enlarge on you, which brings you to gargantuan. You're now a 60ft whale.

Judging from a replica 2 mast ship you are now nearly as long and weigh as much as the ship itself... just push it back to port.

Even without the enlargement, I'd expect you to have no trouble overcoming the push of a gust of wind.

If 9th level is too high (that's enough for 5th level spells), a 6th level Druid of the Moon can turn into a Plesiosaurus (large).

I'd bet even as a large creature you'd be able to immobilize the ship via biting onto the rudder and just swimming in the opposite direction. Bonus points because, with your dino neck, you can be under the boat where most of the passengers can't see/attack you... they may not even notice you're there if you're sneaky enough about it.

No material components, and you can mess with them for hours.