The Museum of the City of New York's online resources include the incomparable Jacob A. Riis photographs of 1880s New York City tenements, and much else for al aspects of city history.
Founded as the Greenwich Village Society for Historic Preservation, this organization's website offers interviews, images, and a history blog about the area between Canal and West Fourteenth, East River to the Hudson.
The Municipal Art Society is New York's oldest organization advocating for the preservation of buildings of historic or aesthetic significance. The society sponsors an annual Jane's Walk in which volunteers organize walking tours of their neighborhoods.
New-York Historical Society
Any one item from the New York Historical Society's digital collections opens a window on the whole city's past. The individuals items are grouped by the source, adding another layer to knowledge about them and offering another launchpad for research.
The Staten Island Historical Society's online collection includes images and images of historic objects in the organization's collections, which focus on Staten Island's past as an integrated mosaic of communities forming a diverse economy
To see if there's a historic society on a neighborhood you're interested in, Google the name of the neighborhood, and search the results for .orgs that may be local history not-for profits.