Recently I've learned of another nautically-themed resource available for pirate-oriented Pathfinder campaigns. It is an adventure, The Ship of Fools, from TPK Games. It's like a floating dungeon, perfect for a lengthy encounter at sea, and it's been well reviewed.
The Ship of Fools
I should note that I haven't read it, as I'm going to pass it along to the GM running the Skull & Shackles adventure path for my group.