Going back to answering the original question. That ~20 year time gap between Crysis 2 and 3, I would assume that Prophet has been around the globe getting rid of the Ceph the same way he did in New York. All that would be left would be the Ceph Remnants.
I guess the only justification of being back in New York is the following... Making a new setting for a video game is kinda hard. Everything from the models to the gameplay. I guess Crytek is kinda rushed to release Crysis 3. They already have the New York models lying around from Crysis 2, might as well reuse them.
I would laugh if in Crysis 3, you pass by a part of New York where you passed through in Crysis 2, like that one level where you have to fight that Pinger at night...
I'm sure they'll have nods to old levels in the game, all overgrown or underwater, at least I hope they do!
The Ceph resurgence in C3 has to be a fairly new thing in the timeline, since I do NOT see CELL building a damned DAM and all the other facilities we see in the gameplay while having Pingers, Stalkers and Heavies raiding the construction sites.