To me, the word 人間 brings the feeling of "humanity", i.e., makes me think of human rights, citizenship and things like moral and ethics.
it seems to be okay to consider some humanoid alien a "ningen", but the same would be inapplicable for a humanoid deity or a common animal (cat, dog, etc...).
A humanoid alien community might very well have concepts of morality/ethics as well, so you could sympathize with them similarly as you would with other humans; you could consider these aliens worthy of kindness, respect, and everything else, thus considering them also humans in this point of view. This clearly constrasts with a deity or an animal, since they are usually not put at the "same level of ethics" as humans.
Example: imagine that an alien ship crashed on earth, and there are a few thousand alien survivors. Some researchers want to deeply study their anatomy, by giving them drugs/diseases and see how they react. Then you could say:
They should not conduct these evil experiments in the aliens. They're not lab rats, they're ningen!
To me, this phrase would be completely fine, even though the aliens are not technically humans. I could be completely wrong though, this is just my two cents on this topic. I'm not even a native speaker.