There are certainly a lot of folklore tales about the ninja and maybe even some historial accounts of their actions, but I think it will be hard to find anything in English about it.
I did a search over on koryu.com and did not turn up anything. In fact, what turned up really point towards there not veing any real Ninjutsu "ryu" per se at all. There may have been individuals that performed guerrilla warfare type actions, but they seem to think that there were no real "ryu" in the sense of a koryu in existence anyways.
Dave Lowry
http://www.koryu.com/library/dlowry4.html
"To meet the grazing appetites of the interested public, there was also no shortage of arts that were more or less concocted, e.g., "ninjutsu," created out of folklore or ambitious fictions."
Diane Skoss
http://www.koryu.com/library/ninjutsu.html
"Simply put, it is our opinion that modern-day ninjutsu and ninjutsu-derived arts are not
koryu bujutsu....That's because we sincerely believe that if your training is working for you then it is none of our business. However, if you come to us and ask whether we consider ninjutsu or the Bujinkan-derived arts to be koryu--well, we can only provide our honest opinion."
Meik Skoss
http://www.koryu.com/library/mskoss5.html
"First of all, as one aspect of the martial arts, the equivalent, more or less, of military intelligence, it is certainly a legitimate area of study. The problem is, except for a handful of koryu, where it's a part of a larger comprehensive curriculum, ninjutsu just doesn't exist anymore. Certainly not as an independent ryu-ha. What is commonly taught as ninjutsu, in Japan and elsewhere, is nothing more than a rather disparate collection of unarmed and weapons arts. This, according to the people with whom I've spoken (people who are either professors of martial studies at Tsukuba University, the International Budo University, and Chukyo University, or headmasters and senior exponents in the classical martial arts), is something that's not very clearly understood by the general public. That's not to say these arts are not technically valid or that they don't have historical provenance. What they aren't, however, is the art of ninjutsu per se."
I for one enjoy arts based on the Ninja. I hope you are able to find good sources on their acts and ways of training.