Haha. I think in a realistic sense...It would depend on the situations. Ninja's aren't exactly open war types. They're the types that wait till you're asleep and slit your throat. In a traditional sense, in an open field battle, Pirates would probably win due to having higher technology that can kill multiple people a shot (Explosives and cannons for example). and overall more modern weaponry (Guns, cannons, explosives, and so on). It's a hard decision to make. Unfortunately, in real life, Ninja's 'abilities' are greatly exaggerated due to the influence of anime and overall mythical stories. They don't have magical powers that can cause them to teleport and stuff like that. So, I think it'd go as thus... If ninjas struck first... odds are they'd win. Since they'd sneak onto the ships and kill everyone when they were sleeping. And those that DID wake up... wouldn't have a chance to fight back too much. In an open battle however, pirates would win.
