Pirates would definitely win, because they have rum or grog which makes them invincible to pain, and the ninjas wouldn't be able to get close because they would catch scurvy and die (pirates are now immune to scurvy, obviously). Also in the unlikely event that ninjas DO kill a pirate, he would come back as a ghost (cuz all pirates do) and steal the ninjas soul. Finally pirates are stronger and fearless and if a ninja wanted to say something he would have to stop and do weird hand gestures, and get killed, but a pirate would just shout 'Aaaaaaaaar' or 'Avast' or 'Ahoy'. Also that would scare the ninjas. Pirates win