the giant building on Vanderbilt between Fulton and Atlantic

What is it? a storage building? the FBI? it has a parking lot on the Fulton side but I never see anyone going in or out of the building.

I think was/is Verizon. So yes, the FBI. And the CIA.

I may be totally wrong, but is some of its office space being used by a business incubator/enterprise center for young entrepreneurs? I thought I had read that at one point.

The Verizon building is a block away on Clinton Ave (next to the Collection 525) -- I think there was a Brownstoner post about that monstrosity on Vanderbilt possibly going residential. Or maybe I imagined it.

Yup. Here's the Brownstoner link.

http://www.brownstoner.com/brownstoner/archives/2008/01/470_vanderbilt.php