While the setting is New York City it should be noted that this is a very different New York City than people are used to. Alien attacks, tidal waves, earthquakes, bombs, missiles, attacks by creatures. These things have a tendency to change the face of a location, and places change. It should be also taken into account that being a fantasy setting that the ST may well have changed things.
For instance, F.A.O. Schwarz was not bought by Toys R Us, it was bought by a private investor who has kept the store open and operating and is getting the iconic toy store to turn a profit once more.
Other places of importance around the city that diverges from the norm are listed below.