I started this, becasue I am sick and tired of the whole pirates vs. ninjas thing. Even today I still find stuff about it. So this is to appropriately put down any more hypothetical nautical/asian battles.
Pirates that we think of originated around the 1600s, when globalization first started to occur. Interestingly enough, a lot of the more infamous pirates (such as Blackbeard) started out as privateers, government funded pirates hired to disrupt shipping of foreign trade. Your cliche pirates really got big around the 1700s, with trading among the Americas, India, and China. They gained further fame through movies such as Pirates of the Caribbean, though most of the cliches in the film were not even true. Basically, pirates were vicious and cruel, and killed, raped, and plundered. They were not the free, fun loving bunch of misfits misunderstood by common society as depicted in Pirates of the Caribbean.
Now on to ninjas. Ninjas start much further back, during medieval feudal Japan. I know considerably less about ninjas than I do pirates, but I know that they were not magic. Often, they were simple peasant farmers fed up with their government. Ninjas also did not wear black, as black fabric would have been commodity too precious for a commoner. Most ninjas actually wore dark reds or blues. However, ninjas did employ stealth, martial arts, and a number of chemical tricks to confuse their opponents. For instance, hallucinatory powders thrown into the face of an opponent could make them believe that they were seeing double, as if the the ninja had mystical cloning techniques (familiar?).
However, the biggest issue here is time and place. Two different types of people from opposite sides of the world from different times could not fight. You might as well ask "Who would win, an Aztec Soldier or a Cassock Soldier?". However, if time travel ever becomes possible, I would pay to see such a fight between a pirate and ninja, but for now, let us safely assume that the two do not exist within the same time frames, and so could not battle without that technology.
Now that you've seen my thoughts, what are yours? Simply put, do you agree, disagree, have a different interpretation, or just don't care?