I went by this site yesterday and I can say that the first two towers of Hunters Point (sites A and B in the map below) are above ground!
Forgive the quality of the images...they were taken with an Android phone:
Looking north along Second Ave, from the edge of the LIRR railyards. The building on the left is the LIRR ventilation building...this will be the future location of Building C. Next is the dark blue-grey elementary school. Right in front of the elementary school you can see a backhoe and a crane base for building B. This building will rise to 32 stories and is already at ground level. Then beyond that you can see the crane for building A, which is already above ground and will rise to 38 stories.
[IMG size]http://i.imgur.com/yx4jT5fl.jpg[/IMG]
Crane for building A:
The work on building B: