I was looking over a real world map of new york and I found a great spot that the map could realistically be located in.
Wall street.
This location is right in the middle of the city, you are able to see nearly all notable landmarks from this location. You can see the statue of liberty and ellis island from the docks, you can see the empire state building in the distance, and players may actually be able to go to locations like wall st, broadway, the trinity church, and the city hall from this location.

The area in the red circle is the main city.
The area in the yellow circle is an infested district that is sealed off from the main city.
The red line is Wall st, and the green line is Broadway.
The blue icon at the bottom of the image is the docks, the blue icon at the top of the image is the Trinity church, it could be an interesting location to have an infestation.
The different buildings and the roads in the circled areas can be changed to different things to suit the maps needs, but even now the spot looks great.

This is a slightly zoomed out picture of the previous image, city hall isnt located far from where this map is set, this could be where the nexus and CCA could be located. The only methods to get to the nexus would be via a sealed off APC tunnel or by taking a train to it.