What happens on the roof, stays on the roof.
It wouldn’t be a Spider-Man film if he didn’t spend some time on rooftops. The majority of these shots included visual effects in some fashion (there’s no way that Sony would be putting Andrew Garfield on top of a giant skyscraper).
These buildings are all shot around Manhattan in New York, and the details of the locations are annotated below.


This image, along with the two above, were shot looking north from a building in the Financial District, though the buildings and streets here appear to be all digitally created. 
These buildings, in this sequence appear to be a digitally created NYC, intended to emulate buildings in the Bryant Park area. 
Peter stands on the lip of the SE corner of the MetLife building in Midtown. 
A wide shot shows more of the MetLife building with Peter perched precariously on the precipice. 
Spider-Man enjoys his lunch on the Met Life building, overlooking 100 Park Avenue in Manhattan. 
Spider-Man lands on darkened roof in NYC, which may be part of a digitally created skyline. 
A police helicopter hovers above a NYC intersection (presumably 6th Ave) in what may be a fully digitally created shot.
MAP
(The Amazing Spider-Man, 2012)