Columbia's Avery Library has research guides on New York City Buildings and New York City Atlases and Land Books.
NYC Planning Department maintains the Primary Land Use Tax Lot Output (PLUTO) files and the MapPLUTO tax lot GIS datasets, available from 1999. Also see BYTES of the Big Apple site for data on zoning designations, LION street centerline files, addressable points, city owned land and facilities, and waterfront related datasets.
MapPluto files also available from GeoData@Columbia.
The NYC Office of Technology & Information maintains a wide array of data in NYC OpenData including building and street footprints, 3-D building models, elevation, hydrology and open space data.
CoreData.nyc : Map based data hub for housing and neighborhood resources from NYU Furman Center for Real Estate and Urban Policy. Includes data from the Subsidized Housing Information Project (SHIP) and the New York City Housing and Neighborhood Information System (NYCHANIS).
NYC Housing Preservation and Development conducts The New York City Housing and Vacancy Survey every three years. Data is available from 1999 from the US Census Bureau and as far back as 1978 from the CU Data Catalog