I recently ran a naval game. I liked it; the big drawback was that to create a believable ship there had to be tons of NPCs, which created a lot of bookwork and took focus off the PCs. I did like the isolation of it, and the focus on weather and supplies and other naturalistic elements I usually overlook.
Stormwrack is a bit of a mixed bag, but I liked the PC stuff (races/classes/feats/spells/gear) and monsters and the narrative naval combat, with a little nudging is good.
It doesn't have any ship-based rules, but Into the Blue is a great monster/environmental book for the seas (and it's 3.5), easily the best such book I've seen.
Seafarers Handbook and Seas of Blood are 3.0; they have their merits but I didn't find either of them nearly as useful as the above books.
Aquatic monsters are otherwise spread loosely throughout most monster books. Likewise, appropriate classes are loosely spread about (Dread Pirate is CAdv for instance, while Seeker of the Misty Isle is CDiv).
I'd also recommend that you have your cartography and weather handled very thoroughly and before starting the game, as these are more important and harder to improvise.