First of all. If anyone watches Mythbusters... the pirate special OWNED!!! the ninja special. Ninjas are shams made by the Asian governments to instill fear in their people so they wouldn't have dared to steal rice from the merchants or others. There is no proof that ninjas even existed, even proving a samurai (side note: how the hell do you pluralize samurai?) is a stretch. Pirates on the other hand, are proven to have existed and kick BUM-BUM. They like...drink rum all day, and steal money. I mean it has to be a lot of money too, right. I mean those ships are HUGE and all those other pirates don't work for free, eh? They probably had one-night-stand-wives that they had to support...which brings me to another point =D. Ninjas can' even reveal their identity, but a
pirate's life is free. Pirates own ninjas in every way.
A pirate would win in a fight because ninjas don't exist, and something that isn't there can't win in a fight. Plus, some have the curse of immortality and don't die. Ninjas are just non-existent, fast-moving, flesh-bags.