It's been clarified that there are no "unchained ninjas". The ninja is an alternative class of the core rogue, not of the unchained rogue.
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Well, despite the fact that it's states that the alternate classes, the ninja and the samurai, are technically archetypes, lately devs have mentioned that this is erroneous and that the classes don't mix with rogue/cavalier archetypes. Mark Seifter has said that he's marked the text where it says they're technically archetypes for errata. So according to the rulebooks right now, you can have an unchained Ninja, but according to the Devs that was a mistake, and shouldn't be allowable, and John Compton has already stated that Unchained Ninjas are not allowed for PFS.
If this is a house game, I don't see a problem as long as you switch out the abilities the rogue normally lost for their new counterparts, ie danger sense. Although the new Rogue actually looks pretty good, and with the new Major Magic trick for the Vanish spell combined with the stealth skill unlock, you can do some pretty nasty damage to creatures who can't see invisible. And if memory serves, you can still take ninja tricks, you just don't get the ki pool.
EDIT - Ninja'd, kinda.
here is a thread on this exact topic with a lot of the info on it.
So there is no such thing as a Ninja favored class?
That's what we're hoping to clarify. It seems many people have worked that you qualify for Rogue FCB and Rogue archetypes that you still qualify for. But now those assumptions are under question.