Running a campaign that's used pirates, I can tell you that you've GOT to resolve 4 issues.
1. Core DnD has never cared for ship to ship combat. You need to figure out a balanced system of, essentially, mass combat or miniatures combat. That's for the captain. Then, you need to figure out what the other three players are going to do. Balancing those two tasks is key. I've pulled it off because I DM a one PC game.
2. Once they kill the pirates, all hell breaks loose in your game. How much is that ship worth? It should be a lot, both because it serves as a good low-level goal (Team PC wants to scrape together enough dough to own their own ship) and for realism (surely this ship is worth more than a horse!). But what happens to your game balance if they sell it? Does it wreck your expected income levels if your 5th level PCs take a poorly-defended merchantman, selling the ship and its cargo? How can it not? And if you make it difficult to sell a ship, then you've got a different problem: The PC Armada. That can be fine... if you've planned for it. Basically, think about the traditional difficulties with giving PCs a castle and add the problem that the castle retainers regularly go into combat, because they're pirates!
3. You need a rational economic system. Your major quarry is the fat merchantman. One of the ways to determine where to find them is by supply and demand. And as soon as the fat merchantman's ship has been taken, the PCs wish to sell their loot. And do you really think that the players are going to buy the idea that it's now worth 20% when the merchantman was going to make a tidy profit on this enterprise? Piracy is about black market economics, amongst other things, and it brings out the mercenary capitalist in players.
4. A mass combat system, not for ships, but for boarders. If your crew dies, you die, because you can't sail home, even if you defeat the Big Bad. Players are going to want to know how their pirates are doing in battle and be able to save them, while DMs do not want to make 200 attack rolls. Yes, there are ways of fudging it, but you need a system that measures how well one force will stack up against another, while allowing players to get involved.