It is hard to compare three great evolving libraries. They all grow and change, but it is good to know what is working now and what isn't.
This library probably is evolving faster than ThreeJS. It is always hard to tell, but they both don't have that many contributors besides their founders. It does look like Babylon had more updates recently and s more active community.
It is worth noting that I did try BabylonJs a few months ago with Google Cardboard and it didn't respond to head movements. I am sure others had better luck then me, but I didn't find so much community support when it came to VR.
AFrame & ThreeJS
It is important to know that AFrame is at its core a wrapper to ThreeJS. It would seem you should favour ThreeJS as you have more control and Documentarion.
If you are developing a major application and your familiar with ThreeJS this might be the way to go. But getting all of the VR code setup for a small project probably isn't worth it.
AFrame shines in its simplicity to have a full project setup and running with only HTML.
Two great reasons to choose AFrame is that the community on slack is Amazing! The next reason is that it is backed by Mozilla which will have more power to affect change than ThreeJS or BabylonJs.
AFrame is the simplest and best product to enter the VR programming world. Especially if it is a small demo project, choose AFrame, I think regardless of your familiarity with other libraries.