In response to a query on the H-Japan list, samurai historian par excellance Karl Friday wrote:
There are basically no publications in English on ninja worth reading–it’s all junk. The only serious academic scholarship available outside Japanese language publications would be the material on Roy Ron’s website at ninpo.org. Roy is a (fairly) recent PhD graduate from U Hawaii, and has spent a number of years doing research on ninja and related topics.
The lack of reliable documents to work with makes ninja and ninjutsu a very difficult subject to research, and the ninja movie and novel phenomenon gives the whole topic a cartoonish aura that further dissuades academic historians from looking into it. Thus there isn’t much out there to read, other than what’s been written by modern teachers of “ninjutsu,” none of whom have an credentials as historians. In English, you’re simply out of luck; in Japanese there a few decent books and articles around, but for the most part information on ninja has to be culled in bits in snippets from studies on other topics.
The most reliable reconstructions of “ninja” history suggest that “ninja” denotes a function, not a special kind of warrior–ninja WERE samurai (a term, which didn’t designate a class until the Tokugawa period–AFTER the warfare of the late medieval period had ended–before that it designated only an occupation) performing “ninja” work.
Movie-style ninja, BTW, have a much longer history than the movies (although the term “ninja” does not appear to have been popularized until the 20th century). Ninja shows, ninja houses (sort of like American “haunted houses” at carnivals), and ninja novels and stories were popular by the middle of the Tokugawa period. The “ninja” performers may have created the genre completely out of whole cloth, or they may have built on genuine lore derived from old spymasters. Either way, however, it’s clear that much of the lore underlying both modern ninja movies and modern ninja schools has both a long history AND little basis in reality outside the theatre. [emphasis added; quoted with permission]
The site which Friday mentions above includes a history section which covers a lot of the same ground as Turnbull (though much more concisely) and some of the primary sources, most of which are either old gunki or 17th century martial manuals.
This pretty much puts an end to the remaining questions I had after reading Turnbull’s book. I used to tell students that the question of ninja was, from a historian’s standpoint, still somewhat open. I think I’m going to take a much stronger line from now on, and point out that there are no historically credible claims supporting the historicity of a tradition which somehow concludes with modern schools of ninjustsu. So, we’re back to the problem of created modern traditions in the martial arts and their discursive meanings.
Update: Peter Shapinsky’s comment about the users of violence and the relative flexibility of the term samurai are also interesting.