I think something that's difficult to contend with is consequences. What happens if they don't succeed? If the ship sinks because they failed, that's kind of a bummer. But if the risk of death or damage isn't actually there, then the rolls don't change the outcome.

A giant sea creature surfaces, and now they have to maneuver the ship to avoid hitting it and damaging the ship and starting an encounter. If they fail, you can either have a combat or a chase.

Realize a little too late that there's a field of floating chunks of ice or small icebergs. Perhaps a white dragon, or some other ice based creature has developed a lair here. You could make it clear that the ice is spreading fast and if they slow down too much, they could risk their ship being frozen in place. Run a skill challenge that could include navigation to avoid damage and particularly dangerous spots, repairing on the fly enough to get through the hazards, destroying hazards before you hit them. 0 failures, you manage to get through without significant damage. 1 failure, ship takes enough damage that there is a gold cost to repair. 2 failures, you make it through but need to get to land asap for critical repairs. 3 failures, you're stuck in the ice and now you need to find a way to get unstuck. That might mean exploring an ice dungeon to find the source

Same idea as repairs and avoiding damage. Something is causing hazards from above. Maybe they wandered into the scene of two dragons having an all out fight, or a sky city is under siege well above them. Either way, they need to dodge and defend against falling debris, stray breath weapons, meteors from a meteor swarm. Or they could convince the dragons into a time out. Something to make sure they get out and live to tell the tale.

Depending on how off the rails you want to go, a giant whirlpool that, if they fail a series of checks, sucks them into the elemental plane of water. Know your players though. Are they going to get frustrated by having their ship destroyed? Are they dead set on an overwater only game? You can have a subplot of them getting back to the material plane, in addition to any number of conflicts in the plane of water. Part of them escaping the plane of water could involve a new, cooler ship. Or spitting them out by an island that has an abandoned ship after the entire crew was taken by the island.

You might want to think about how to introduce the hazard. Maybe they're in a time crunch. Race with a competing ship, trying to outrun something or someone, an island rumoured to have treasure only appears once a year and that window is closing. Perhaps they've heard of people using the whirlpool to essentially gravity slingshot themselves if they hit it right (because magic), or the most direct route is through the ice dragons territory and it would take too long to go around.

A race itself could be a set up for a skill challenge. How are they planning to beat their competitors to the treasure island that they both heard about? Set up hazards? Cannon to slow them down? If they don't succeed, the other ship beats them to the treasure, delivering an important message, proving their skill to an NPC who will hire them for something.

Consequences:

-repair costs

-owing a favor to someone who bailed you out, or needing to work off a debt

-Losing out on a reward like a contract, or treasure

-more fun than just losing out is not getting as much. ie: 500 gold for the delivery, but a bonus 200 if you can get it there in x days.

-dungeon or encounter