Ah yes, the ongoing struggle of awesomeness: Pirates vs Ninjas. Will a victor ever emerge? Probably not, but that's not a good enough reason not to take sides or speculate. The debate was brought to the forefront several years ago on the internet, although the exact source or sources of the initial conflict are unknown. There is little to no official canon to refer to, but there are many websites where the battle still rages. And there's also a pretty kick-ass movie.
There are many questions one must ask oneself before choosing a side. One of them is not: can't pirates and ninjas team up? If that were to happen, the universe as we know it would implode as two of the deadliest, coolest powers in all of existence were joined together. No, theirs' are two opposing fates - they are destined to fight until only one side remains. Much like Highlander, there can only be one. But that's for the best. If they're busy fighting each other, there's less time for pirates and ninjas to plunder and pillage, spy and assassinate, respectively. Really it's good for everyone.
Now, the first and (hopefully) most obvious consideration to be made is fighting ability. According to the movie, they're pretty evenly matched. Both are usually adept at swordplay and hand-to-hand combat. Pirates can brawl with the best of 'em and ninjas are martial arists. While there are exceptions, pirates are generally more brawny and heartily built and ninjas are smaller and more agile.
One flaw I would like to point out in the short film is that pirates can and would use pistols, as well. It's not a question of honor or compunction - they just would. Likewise, ninjas were usually at least amateur chemists and could assemble primitive smoke bombs and the like. Their darts and shuriken would certainly be employed, as well.
I think I will leave this one open to further debate, as it's not clear-cut. However, I tend to think that without the element of surprise (a ninja's greatest advantage) the pirate would have a huge edge. Perhaps this is why rules and circumstances would need to be in place for such a duel, and why this struggle may ultimately never be resolved. Despite what the video games and movies may have you believe, ninjas were meant to kill without engaging in combat. The majority of their skills and training were focused on infiltration and killing without being detected, and therefore without actually fighting anyone. Pirates, on the other hand, lived and died by steel and flint. They had to be ready to fight at any time. Even while drunk, you might ask? Especially while drunk.
So while I would award Part I, fighting ability, to pirates, I will leave the matter for each to consider in one's own heart of hearts. For now, I will leave it at that.
'Til later then.