New York has more Nike stores than I expected. So I mapped the ones worth your time. You get two giant flagships in Manhattan for new drops. There are also factory and clearance stores in every borough. Those outlets are where the real bargains hide....
Map
The big five-floor flagship on Broadway. Great for new drops and custom fits.
Nike Soho
The Fifth Avenue flagship with six floors of gear. Sneakerheads could spend hours here.
Nike House of Innovation NYC
Inside Brookfield Place downtown. Calmer than SoHo and easy to reach after work.
Nike Battery Park
A solid Brooklyn stop near Barclays Center. Good stock of running shoes and basics.
Nike Atlantic Center
Right on 125th Street with real outlet prices. I always find a deal here.
Nike Factory Store - Harlem
A big factory store at Gateway Center. Worth the trip for cheap sneakers.
Nike Factory Store - East New York
The Bronx outlet at Bay Plaza. Kids sizes are usually well stocked here.
Nike - North Bronx
Inside Empire Outlets by the ferry. Pair it with a free harbor ride.
Nike Factory Store - Staten Island
The clearance store at Sky View Center. Prices here drop even lower than outlets.