First, there are pleanty of Pirate themed books out there for you to plunder. Skull n Bones and all the Freeport books being some of the best, but there is alos Salt and Seadogs for Kalamar, the aforementioned AEG Swashbuckler, and some others. Really, any setting that has a detailed port will work, although some of these books will help with mechanics.
If you can find it read On Stranger Tides by Tim Powers, the inspiration for Skull n Bones.
However, I have a couple of suggestions if you want the PCs to run a good/neutral pirate ship.
1) Set up an area of the world where there is a great deal of wealth that needs to be transferred to another region.
2) Set up competing nations/factions for that wealth.
3) Make sure that the main strenght of these factions is in that far off region of the world where the wealth may be going.
Into this setting throw the PCs in a fairly prosperous but corrupt town ruled by a govenor appointed by a far off king. Said king wants the gold/source of wealth or knowledge/whatever that a rival king has been moving from this region to fund his own plans to expand back in the homelands. While piracy is frowned upon by any lawful nation, privateering can be another matter.
Privateers are basically naval mercenaries who recieve a letter of marque (mark) that gives them legal powers to stop and cease ships of a certain nationality or in a certain area. Perfect for your PCs. The question then becomes how closely do they fall the details of their letter, and do they attack other kinds of ships and engage in other possibly illegal activites?
Some ideas for adventures
- Have the PCs begin by proving themselves to the govenor/local official by rescuing his daughter (a cliched but classic example of swashbuckling, vary it by making it a court official come from the homelands to check up on things) or capturing a wanted criminal who has recently escaped hanging.
- Once they have leveled up a bit they can be rewarded with a Letter of Marque and start hunting the Dread Pirate X or harrasing the ships of Enemy Nations.
-Build up a main pirate bad guy. Have said pirate bad guy be in league with some native mystical powers who can field undead crewed ships, summon up sea monsters, and hunt for ancient artifacts in lost temples.
Whatever you do, be sure to encourage your players to build PCs that have skills that are useful on a SHIP! MAny will just focus on the combat aspect and you will have no logical reason to ever put them in command of a ship.
Oh, and buy a few packs of Pirates of the Spanish Main Cards ($4 each) for nifty ships and islands that you can use in your game.