One of the most comprehensive collections on Brooklyn history.
New York Historical Society
Established in 1804 as New York City's first museum, this has a comprehensive collection focusing on New York City history.
The Museum of the City of New York
"The Museum of the City of New York celebrates and interprets the city, educating the public about its distinctive character, especially its heritage of diversity, opportunity, and perpetual transformation."
Bronx Historical Society
Preserving Bronx history.
The New York Public Library's Digital Collections
"Explore 729,730 items digitized from The New York Public Library's collections."
Additionally, you can explore (and visit!) the New York Public Library's Research Divisions here.