Thanks, e2efour. The following site shows a floating boat under the title 'how to draw Boat in the sea.' Is it not common?In the sea suggests to me that the boat is sinking. We can say that a boat is low down in the water, but we normally say I can see a small boat on the water.
But it's difficult to say what your phrases really mean unless you give us a sentence!
Thanks, Parla.It's not ambiguous, nor is "on" a mere preference. "In" is incorrect unless the sailboat is sinking, which it doesn't appear to be.
I think that the text was probably not provided by a native speaker of English. The sponsor of the how-to-draw site is apparently a German firm with affiliates in various European and Asian countries. (This information appears only after digging through a number of links and sub-links.)