I think it depends a lot on where you are. You aren't supposed to have firearms in State Parks, not sure how that applies to waterways and rivers and stuff that go through State Parks. I am interested in the answer on this one, too!
You need a permit to carry, plain and simple. There are always places with a permit that you still cannot carry, schools, court houses......but boats are not one. As long as u have a permit u should be good to go. (CT waters)