Since the "Ninja Boom" of the 1970s and 1980s, countless people have come out of the woodwork claiming to teach ninjutsu. Most of them are full of it, but that doesn't mean they all are. In the last couple years, several people as part of a research team on historical ninjutsu have demanded these people show their documentation. The claim is basically that authentic shinobi no jutsu is dead, and the feudal era over, therefore in the interest of research and authenticity, they should have no problem showing their scrolls to the world to prove their legitimacy. But it's not as simple as that.
Not to mention that carrying around written scrolls would be evidence of espionage and would probably get you killed if you were caught! Not really a great incentive to write things down.
I have my own opinions on who is legitimate and who is not in the ninjutsu community, however that's not something I will go into because I don't know for sure. At the end of the day, that's perfectly fine. I am not a ninjutsu instructor. There are well defined parameters to what ninjutsu is and what it isn't. The only question you need to ask is if what they are teaching is in line with historical ninjutsu. It must be learned through direction transmission so, just like the controversy in the aiki community about who "has it" or not, the origin becomes less important because it came from somewhere. This is because ninjutsu is not a hand-to-hand form of fighting but rather a set of skills required to carry out various missions. These skills encompassed disguise, espionage, military strategy, fortification, survival, divination, meteorology, witchcraft and more. These skills, collectively called the ninja juhakkei, would have to be learned in addition to the regular arts of the warrior class including martial arts.
So, when you're looking for legitimate ninjutsu this is what you should be looking for. Does the school you're interested in teach only fighting arts or are these skills (at least partly) taught within the curriculum at some point? Do not expect to be exposed to legitimate ninjutsu on your first day, (and to be honest, most people don't want the okuden level ninjutsu anyway) but there should be tell-tale signs. While documentation is important, the content of what you teach is more significant in my opinion. In a court of law, the burden of proof falls upon the plaintiff, not the defendant. Can you disprove their claims beyond a reasonable doubt? If not, then you're not in any position to publicly try and discredit them.