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.
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.
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.