Does any movie or game actually portray ninjas accurately, or is it all based on the legendary ninjas that had little, if anything, to do with real history? As far as I'm aware, real-world ninjas were more similar to modern spies, trying to dress as inconspicuously as possible (the black ninja suit we're used to from legends would stick out like a sore thumb, so no actual ninja would be stupid enough to wear one) and using subterfuge more than actual stealth. Combat wasn't really their forte.
Since the OP is asking about the best depictions of Ninjas, I would consider a historically accurate depiction to be a worthy candidate. Is there such a thing?