Well Gumer, I'm afraid I must challenge your decision, because you know I can't resist a good ninja debate. But rather than trying to use a logical or historical argument, I will use one of pop culture:
Ninjas make up a huge part of our culture and entertainment, from generic stock villains, to central characters in film and games. Particularly from the game angle, there have been many ninja based games, and adaptations which could be categorized as a "ninja themed" basically describing any games that use stealth as the central focus of the gameplay. This would include all spy games and one could even look at spies in film and game as forms of modern day ninjas (making Sam Fisher from Splinter Cell and Solid Snake from Metal Gear Solid both modern day iterations of ninjas). They use stealth, subterfuge, and technology (ninjas used high technology for the standards of their times, resourcefullness, as well as non-conventional methods to accomplish any task set before them).
Now on the converse, there has been little contribution from pirates to our culture, and about the best example to arise from the pirates in entertainment has been, ahem, Pirates of the Carribean.
So while both may still be badass (or stupid, however you want to see it), I'm afraid ninjas seem to have the advantage. I now welcome a rebuttal, but bear in mind I haven't even pulled the big guns yet.
My real question is who started the whole ninjas vs pirates debate in the first place? I mean, who even saw a connection there? I could see samurais versus cowboys based on all the social and cultural parrallels they represented, but ninjas and pirates? Oh well, should be fun to see where this goes (if anywhere).