Originally posted by Seaside:

Would be nice if there was a sit/freeze in place option for Boars/Wolves etc. to stop them from jumping overboard. It might stop the clipping you are getting as well.
Since you can't build on a boat I doubt there is another option unfortunately.

Only other thing I can think of is to keep your players jammed into the stern so the boars can't get there but I'm sure you tried that one.

The best suggestion I saw for this was for the devs to include pokeballs to use to move tames around.