Haha, I have this debate more-or-less every day with my friends. XD
Personally, I prefer ninjas. xP Because ninjas are smarter, better fighters, and a lot cooler. ^_^ ((And pirates smell. xPPPP))
Also, if there was a fight between a pirate and a ninja, the ninja would win. While it is true that pirates have guns, ninjas are good at dodging. So, the ninja would dodge the bullets and then throw shuriken at the pirate, hitting the targets, and so winning the fight. xD
-"There's a hole in the world like a great black pit/And it's filled with people that are filled with sh*t/And all the vermin of the world inhabit it/But not for long..." - Sweeney Todd.