Until the Blu-ray comes out or we start to see Odd Creatures talk in more detail, I don't think we'll know for sure. They had an Alien on set to perform, we know this. They were told at the test screening that a lot of the creature effects would be supplemented with CG and most of what I saw looked CG to my eyes (apart from one sequence with the head).
There's also a shot in the b-roll footage where we see a stand-in for the Neomorph doing his thing. We won't know for sure for a while.