I think pirates are better for their strength, and spirit! YARR!!! It may be due to the rum, but pirates clearly have more motives going for them. What do ninja's have to fight for? Pirates have their pride and often times treasure. That, and having a parrot on your shoulder that talks is pretty awesome. Sure ninjas got sneaky ways, but pirates do as well, and they also have more weapons as root mentioned.
EDIT: Muz also gave a good point....she is quite the hottie