My advice would be to start with basic, non-themed items in the right color scheme and then add a few key elements that turn it swamp-y... that way you don't have to completely redo everything in a year or two when he's not so into swamps... or you can remove the theme-y stuff and it'll be a nice big boys room.
Most of the boat beds I've seen are sailboats or pirate ships... not very swampy... If you're very handy, you might be able to take a real rowboat apart and make something, but if it were me, I'd go with bunk beds and bring the theme in elsewhere.
There's a paint color a friend used in her house called "cash green" or something like that, which could be perfect for your walls.
A beige or khaki bed spread would work and natural wood furniture.
THEN look for wall decals with swamp pictures.
Get some actual photos of alligators, enlarge them and hang them in light weight frames on the walls.
Use some camo fabric to make a couple of throw pillows and window coverings and that should be plenty to take the pattern around the room.
Maybe a swampy throw rug too.
Good luck with this... you'd be surprised how much theme a room can take on with just a few pieces.