Office of the City Register
"The Offices of the City Register maintain the New York City public records for the Bronx, Brooklyn, Manhattan, and Queens. These records include Real and Personal Property transfers, interest, and ownership information." - City of New York
Recently, I needed to check out the history of ownership for a property in Manhattan, so I took a trip down to 66 John Street to look at the records in person. Some of the City Register's records are accessible online, however, you can save a lot of time by browsing the originals or microfilmed versions at their locations around the city.
I've also visited the City Register in Brooklyn to examine mid-19th century mortgages, which are not available online. Strangely, the Brooklyn office only has microfilmed versions of many Kings County records. The originals live at the Office of the City Register in... Queens! Makes total sense when you think about it.
Actually no, it makes no sense, why do people do these things?
If your ancestors owned land in New York City, check out their county's City Register office (addresses at the link). Here's a map showing the Manhattan location (double-click to open in Google Maps):