We've covered the tricky problem of the Ninja several times here, most recently in this thread, with u/NientedeNada, which explicitly considers popular perceptions, the authenticity of the sources most commonly cited in this respect, Stephen Turnbull's recent reappraisal of his views on the subject, and the inadequacies of our own FAQ on this topic:

What exactly is a ninja and what was it like being one in medieval Japan?