Black Tiger: ahh, gotcha. i've played and beaten all these games at some point, except for Ninja Gaiden III of the trilogy... that's some intense shit.
I had to go with Ninja Spirit. It's just a damn fine port of a damn fine arcade game. Yea, it has some run-n-gun elements, like Contra, when you use the stars or bombs, but imo that's an awesome thing.
Shinobi III is awesome too, and it's close between Ninja Spirit and Shinobi III, but I have to go with Ninja Spirit. It's just all-around badass... especially for an early title.