The most famous historical ninja of all is Hattori Hanzo. Of course, there's no actual record of him having been a ninja, only that he was a samurai from Iga (one of the two homes of ninja, the other being Koga) who served under Tokugawa Ieyasu.
You can find all sorts of factual and fictional accounts of Hanzo. And pretty much any manga or anime or movie made in Japan will either have the man himself, one of his descendants (who of course have the same name), or at least someone named Hanzo or something similar.
Hanzo as he appears in the video game Samurai Warriors.
And if you've only seen Kill Bill, well, he was not a swordsmith (although they do imply that the Hanzo in the movie is a descendant of the legend).
As most historical records that even mention shinobi only have references like, "a shinobi entered such-and-such castle and set a fire," actually having a Man of Iga on record, sort of, makes him a ninja superstar!
Okay, maybe not quite that big of a superstar, but hey, it's Bootsy, baby!
Well, anyway, if you're gonna have ninja in your game, learning the accounts of Hattori Hanzo, both historically verified and fictitious, can only help to improve your game and your ideas about what ninjas were, and what they could be.