I don't know about ship-to-ship, but we've been playing a lot of Freebooter's Fate recently for pirate skirmishes on land, and it's excellent.
It has some very light fantasy elements, which may not delight the pirate purists, but it's fast and great fun, with simple but comprehensive rules for fighting (bluff-based card combat, which includes rules for sneak attacks, reloading, overwatch actions, ganging up, shooting into melee, morale, fear, etc.), swimming, climbing, jumping, carrying/activating items, and more. The models are great too. Highly recommended.