Madison Square Park is located in the Flatiron District, and mostly comprises a quarantine zone and some clear areas.
Most of the area is surrounded by barbed wire and gates, while you can access it from the southwest entrance only. Once inside, there are many holes with body bags being burned, and bulldozers ready to put more into said holes. To enter, have a filter level of 3 or above. It looks to have been a mass burial site like most parks in the game, and its close location to the Dark Zone helps this theory.
There is a Virus Research encounter for the Medical wing there. If you are doing the virus research, look into the ditches, as they hold the virus stations. Once you are done, go back to the entrance and upload it to the server.