While I don’t have much information about the history of the New York City transit system, there are sites that do.
This site began in 1995 and contains a treasure trove of historical information, maps, photos, and documents of the NYC subway system – from its beginnings in the late 1800s/early 1900s to the present.
This site has been around for quite a while and focuses on transit photography across many subway and other rail systems in the US and Canada, but also houses a mainstay section on the NYC Subway System.
Other sites will be added as I locate them. If you have a historical site that covers the NYC subway that you’re aware about, please let me know!