I don't see any access to the closest rooftop in that picture, so I would guess that it's a glass box covering a stairwell. I'm not familiar with the architecture of New York buildings though, so it's merely a guess.

Believe you're correct, as there appears to be a faint outline/shadow for a handrail as well, at an angle that would be used for stairs

Currently out-of-service greenhouses, maybe?