So besides the fact that pirates have the benefit of an easier training regimen compared to ninjas, and the pirates also have a Major League baseball team named after them and yet no one is planning to name a new NFL franchise "The Los Angeles Ninjas", among other cultural advantages, what else is there to measure ninjas and pirates? It really comes down to who will win in a fight.
Now, ninjas of course are quite formidable, what with their sneaking around and their variety of silent but deadly weapons. Chances are, a ninja is watching you right now as you read this. (And yes, your secretary is very likely a ninja at night so don't piss her off) Ninjas are known for stealth and ruthlessness (which means no one named Ruth can ever date a ninja) and an uncanny ability to hide in ventilation shafts. (This is also why there are no fat ninjas, and don't bring up that awful movie "Beverly Hills Ninja" because Chris Farley's corpse has suffered enough) I think I'd much rather have a pirate coming after me than a ninja, because then at least I could try and bribe the pirate with rum and candy. Ninjas? They can't be bribed. AT ALL.
However, this all changes the minute you are at sea. Ninjas are notoriously seasick, which is why they stay on land (and the original ninjas couldnt' leave Japan, since it was an island at the time. Yes, Japan is a peninsula now). Pirates operate best when they are "on the briny" and see some "scurvy dog" on the horizon, and hope to find plenty of "booty" on the other vessel (ships full of treasure were considered especially "booty-licious"). Next time you ride a Carnival Cruise ship, ask yourself whether you'd rather see a pirate boat on the horizon or a ninja ship. The pirate ship meant you were about to walk some planks and give up your loot. The ninja ship meant you were going to be nursing some seasick ninjas for a while.
I need not point out for you that oceans cover most of the surface of our planet, so this is one big advantage for the pirates. Now, in terms of weapons, ninjas have better swords, but pirates have guns. So long as the pirates don't wander into narrow alleyways or forests, the gun gives them a decisive advantage. And when's the last time you saw a pirate in a narrow alleyway or a forest? That's right, never.
On the whole, it looks like the pirates win yet again.