Ninjas have martial arts skills. They often carry with them a bit of mystique. They sometimes have really cool weapons or may possess magic abilities. Sometimes those abilities are more hokey than anything else, but that can add to the charm.
With pirates, they're just thieves with swords. Of all the adventurous stock characters, they're among the least interesting in my opinion. I guess people just really like the vicarious thrill of taking what isn't theirs because there isn't a whole lot to them beyond that.
Well Ninjas live like freakin' monks, and pirates live like free adventurers. ---
