I did a quick google search for famous historical ninjas, and chose Fuma.
http://en.wikipedia.org/wiki/F%C5%ABma_Kotar%C5%8D
According to wikipedia, successive leaders of the Fuma ninja clan each adopted the name of Fuma Kotaro. It seemed in keeping with the spirit of the game to choose some kind of historic figure for the role.
As for your book reference, I've not read it. Is it good?