Ninjas all the way. You don't need to be stealthy at all times to be deadly. They're master's of Ninjutsu so with any weapon or hand to hand... the pirates are fucked. Muskets are inaccurate weapons that lob balls of iron... however ninjas are trained in deadly accuracy with throwing knives, stars, blowguns, and straight up bows and arrows.
The only scenario even remotely doable for the drunken pirates would be to be sitting on their ship off shore and lobbing cannon balls all over. Even then, the ninjas are smart enough to find a way around them. Shit, it's been said plenty of times that ninjas were seen running on top of water. Ninjas are life-hackers.
Plus Ninja Assassin was fucking tits. Never seen a homo pirate movie come even remotely close to being that wickedly win.