If you're talking about a 20-40 footer that is under way, you're going to get a lot of motion no matter how calm the waters. In those cases I use a wider lens so that I can crop and straighten in pp and a faster shutter speed to reduce shake. Oh yes, I also keep the camera on the strap (Black Rapid) so there's no chance of dropping it overboard unless it's following me down.

If you are asking about a ship like a cruise ship, then no special adjustment is necessary unless you're in particularly rough waters.