Ninjas definitely would own pirates! Cause they can sneak around and have razor sharp swords when pirates have their stupid playthings! Plus Ninja's are faster! Ninjas own all!
You know, I have had a battle of this between me as well. I mean, ninja's are cool n' all, but only in anime, and pirates are awesome in movies, but in real life they were coldblooded relentless killers, pillagers, and hired guns who never bathed.
pirates are specialized in killing other pirates and ranged battle. their melee battle talents are kinda below 0. ninjas can sneak, kill them easily, and then, using basic navigation, go back to the shore.
also, ninjas get more money. assassinating, doing missions and stealing earns you more than digging for treasures and sinking ships!
Normally I would have chosen Ninja's because they don't die often, but if I make the comparison with anime then it's One Piece (Pirates) VS Naruto (Ninja's) then I really prefer the pirates because they have more fun.