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).
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.