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Uh, real ninjas and real pirates, or make-believe ninjas and make believe pirates? Make believe ninjas, of course, they can shoot from their finger tips. Real life pirates, they have guns. :P You can't really sneak around on a bboat. now maybe, if the pirates had gotten drunk or something. Or maybe, they are asleep.
If you haven't gotten my message, it all depends on the situation.
There should be no question here.
Ninjas.
They're smarter, more able, and they are just plain better in every way. Seen 'Ninja Assassin'? Lol. No pirate could stand up to that.