Waterways are public as long as you stay in the boat. Once you get out and touch the shore or river bed then you're on private property. That's not to say there aren't other regs that apply depending on your location, i.e. LBL & their permits.
I don't know about the distinction between types of firearms though, that's a good question. The hunting guide doesn't appear all that clear on this issue, at least the way I read it. If you talk to F&W let us know what they say about it-