Ninja's would win of course! Pirates wouldn't even be able to see what hit them before its too late! Only way they would see or know is when the pirates head has been sliced off their shoulders by the Ninja's sword, and fallen to the ground, Only to see with their one eye that their body is still standing there headless... and while their hands haven't even got a chance to grab a hold of their pistols yet.
So there..... Ninja's