The route in New York City
I am not familiar with New York City.
Brent and Nova enter the underground tunnels at the Queensboro Plaza subway station. Which apparently is an elevated subway station in the boro of Queens in real life. The subway line to Manhattan takes the 60th Street Tunnel, which should reach Manhattan about 60th St.
Later they seen the ruins of the New York Public Library main branch. which is at 42nd St. and 5th avenue.
Later they see the ruins of the New York Stock Exchange, at 11 Wall Street and 18 Broad Street in lower Manhattan.
Later they see the ruins of the Radio City Music Hall at 6th Ave. and 50th St.
And then they come to a street sign which says 5th Ave. and E. 51st Street. They enter a church there which is supposed to be St. Patrick's Cathedral.
So it would have been logical for them to pass St. Patricks Cathedral, then the Radio City Music Hall, then the New York Public Library, and then the New York Stack Exchange. And then they coud have found a nearby church, like Trinity Church. The interior set of the chuch in the movie looks like it was much smaller than St. Patrick's Cathedral and closer to the size of Trinity Chruch.
But instead they enter Manhattan about 6th St., trave south past the New York Public Library, and a few miles south to the New York Stock Exchange, and then turn around and head back northeast, passing the Radio City Music Hall and then go to St. Patrick's Cathedral.