The Xenomorph is definitively up there. Can't think of a better Monster villain that embodies the Otherness so perfectly.
John Carpenter's Thing is also amazing in that regard. His concept works so perfectly in the setting where it was introduced that it definitively deserves a nod. You could say It works as a good counterpart of the Xenomorph, making you see the Otherness in people.
Now, the third one should be a villain of a different nature, I'm thinking O'Connor from 1984's adaptation or Frederick, the Minister of Interior that reprograms Alex in A Clockwork Orange. I'm struggling to find a character that personifies this kind of dehumanization (Palpatine definitively operates like this) but it's definitively the kind of thing I'd indulge into this list.