Recently on the Samurai Archives Forum, there was a discussion about making the myth of the ninja the subject of a future podcast. Part of the discussion centered on just how the myths of ninja clans such as Koga and Iga came into being and the image of the black-clad super assassin found its way into Western pop culture. Writer Stephen Turnbull and 'ninjer master' Stephen K. Hayes were two popular suspects.
Actually, the whole ninja craze in the West got started with the 1962 Japanese TV series "Onmitsu Kenshi" (Spy Swordsman), which featured the titular character fighting hordes of ninja clans through 10 seasons. It was dubbed in English and released on TV as "Shintaro The Samurai" in Australia in 1964, where it became a super smash hit on the level of the Batman TV series in America. The actor who played Shintaro (Ose Koichi) did a live action 'concert tour' of Oz and got bigger crowds than the Beatles. Kids in Oz emulated the ninja (leading to a Superman-like disclaimer that they shouldn't be trying this at home).
Then things really caught fire with the 1967 James Bond movie "You Only Live Twice" (where Bond masterfully passed himself off as a native Japanese by getting his hair cut and having a couple of prosthetic eyelids glued on). Tiger Tanaka's sekrit ninjer organization was based in Himeji Castle. Himeji let them film on site but regretted it when the film crew started tearing up the woodwork with throwing stars-the castle had recently been completely disassembled and restored and had just reopened, and those damn ninja were tearing it up!
Mainly because of the movie, phony ninja masters (like Hayes) began to pop up in the late 60's and 70's, spreading their crap among gullible would-be martial artists. And then the 1980 'Shogun' miniseries came along with the 'Amida Tong' (hoo boy-I've seen this cited online as an historical ninja organization) and hordes of ninjer and there was no turning back-the dam broke. It gave birth to all those Sho Kosugi movies, American Ninja, dumbass Ric Meyers and his series of ninjer novels and film disinformation, Eric Van Lustbader's execrable 'Ninja' series of novels, and oh so much more. Turnbull really just 'rode the wave' of all this.
Historian Pierre Souyri wrote "The World Turned Upside Down" in the late 90's. It's a very well written history of Japan from the Genpei War through the end of the Sengoku. Syouri looks at all levels of society, not just what the daimyo were doing, and has a lot of info on culture,art, and politics. He includes a short chapter on how communities in the Iga area formed self-governing collectives during this time. Combined with the rough terrain and remoteness of the area, they were highly successful in doing so. As fellow mod LtDomer mentioned, it does show how the whole 'ninja clan' myth got started. In reality, they weren't much different than Ikko-shu groups minus the religious element.
So there you have it-a short examination of where all the disinformation surrounding ninja in the West got its start. Japan is obviously a major culprit in this as they too have a long tradition of fictional ninjer nonsense which both fueled the Western version and in turn was fueled by it.