It's clear that the pop cultural image of a ninja is at best, an exaggeration and at worse, completely false. But I've read about them using different sources and I still don't have a clear picture of what they really were and different sources give me different answers. Were they simply samurai using guerrilla tactics? Were they an order with secret mountain villages for training? Were they just people hired to spy and assassinate? Were they peasants secretly resisting the hierarchal society of Japan? Or were they something else entirely?
I'm a ninja skeptic. Depending on what people mean by ninja, they may not have existed. "Shinobi warfare" ie. all the sneaky, underhanded parts of warfare is a real thing, but as I've commented before:
There is no doubt that "shinobi" warfare existed, it's documented from one end of Japan to another over centuries. And there is also no doubt that certain individuals were good at it and worked for their masters' benefit. Some of those individuals were indeed Iga and Koga people.
The key issue with the ninja tradition, though, is a) was there a particular Iga and/or Koga tradition of shinobi warfare, famed outside Iga and Koga? and b) did Iga and Koga warriors skilled in shinobi warfare ply their trade outside of their own territories and local wars?
I don't think there's actual existence for either of those things.
There's more elaboration on the problem of "ninja" in my posts to these threads: How many koku would a ninja in medieval Japan get paid for a typical assassination? and its follow-up Were there actually female ninjas. As explained in those posts, plenty of the individuals identified in legend/history as practicing shinobi warfare were samurai.
As mentioned in those links, the key paper in adding to the English language information about ninja was Stephen Turnbull's The Ninja, an Invented Tradition? which I haven't seen any rebuttals to, and a lot of historians relieved that Turnbull's made up for some of his earlier over-eager readings.
In the FAQ there is this excellent answer by /u/AsiaExpert on ninjas in general