You should be able to export your animations as baked animated FBX from Unity. I haven't used it in a couple of years, but I remember there was an option to bake your textures to the model, then check embed textures in the export options. The other option might be to save your animation out of Unity as an animated sequence or movie file, then composite over the footage in AE as you would any other compositing job. You'd have to make sure perspective and camera angles matched up properly, which could take some effort.
If you export as FBX animation, you may need the FBX to AE plugin to import animated objects and cameras and have them automatically linked to reference solids and nulls for AE compositing.
Again, I haven't done that in a while so I don't know how AE handles FBX animations in new versions, but a couple years ago, that FBX plugin was great.
