Living Imagination's Pirates! book is good if you're looking for NPCs and villains. There are a number of good archetypes, some historical, as well as a variety of fantastical characters. There are also good rules on the business of acquiring, maintaining, and running a pirate ship.
I'll also add in the nod to Broadsides! as the best ship combat rules, though be forewarned it is a lot of crunch for ship-to-ship combat (no pun intended!).
For additional fluff and general shipping stuff, check out AEG's "Ships and Sea Battles", a supplement for their d20 port of 7th Sea. It is tied to the 7th Sea campaign setting, but has a lot of good, basic information on ships, shipping, nautical culture and business.
Carl