I ran gunboats (RAC's) in the USMC, and can tell you that even with a 240G or an M2, it's tough to hit accurately off of a rocking boat, or even one running "on step".
I'd recommend something that shoots a rifle round with some power, that may penetrate the bad guy's boat and/or fuel tanks. that means a 308 or 30-06, probably at least. 7.62x39 is a maybe.
I'd also pick something you can disassemble completely and drop in oil at the end of the day. let it soak for an hour, then go at it with a stiff brush to knock off any surface rust that may have accumulated.
I'd lock a pelican case to the running boards, using carbiners if possible. a plastic coated chain or steel cable might be a good second choice, stainless if possible.
my choice would be an M1 Garand, based on cost, ammo availability and performance (even AP rounds), ease of disassembly, availability of parts, and reliability of the weapon. no sense in having the world's best weapon turn into a single shot b/c the magazine turned into a hunk of rust.
after swimming with an M16A2, I can tell you salt water is tough on mags and any spot you can't reach with a cleaning brush and CLP