As much as I hate to say it, ninjas would win in a fight. Ninjas are invisible, breath fire, can fly and don't need oxygen.
Even with the disadvantage being very much corporeal, requiring oxygen to maintain homeostasis, and their lack of being able to immolate people by yelling at them very loudly, pirates would still put up a pretty good fight.
Oh yeah, I also forgot to mention that ninjas have Kinoki footpads, which are based on the ancient Japanese technology of sucking all the heavy metals out of your body by pouring vinegar on your foot. Pirates are loaded with nasty heavy metals.