If any of you go with the Havaheart trap, be sure to put something under it, like a plastic tote cover or the like. The temperatures on a covered boat will cause an animal to expire and getting the smell of that out of a boat won't be easy or cheap.
Sticky traps for rats with food in the middle might be worth a try. I would put a bunch together screwed to a piece of plywood or something. That way they will stay flat and stay put. You don't want to get that sticky goo on your boat!
Rat traps, baited with something tasty might be worth a try, again, I would screw them to a board.
Squirrel Control
Predator urines such as fox and wolf urine are an effective way to keep squirrels from returning, but squirrels are smart and will watch for these predators and will possibly come back.
Good luck. Keep us posted on what animal this turns out to be and what worked.