Crystal Dynamics has been working on a "New IP" for a while, whereas every other New IP at Square Enix was canceled, so if we assume it really is a Marvel announcement, I honestly think it would be them.
Eidos Montreal by comparison just shipped Deus Ex, and is heavily rumored to be making Shadow of the Tomb Raider, so I don't think they would have the bandwidth to handle it.
The other option that comes to mind is Avalanche (the Just Cause people), who have had a long time relationship with Square Enix, and were previously working on an Iron Man game that got canned a while ago. They could be working on a variety of Marvel related games.
The other other option is that Square Enix is publishing a Dontnod (Remember Me, Life is Strange) Telltale-style Marvel game similar to how we're getting Guardians of the Galaxy.