Why not just use an Animation?
If it is a movie - try to simulate it
If it is a game - fake it
If you develop a racing game, you would use particles to Show some Kind of dust behind the cars. But would you take the wind direction into your game? I don't think so.
Just use some different idle animations for a boat in small waves / big waves.
Well if your game is a kind of "SIM Sail Boat", you could be forced to throw some math into your game.
Just an idea...