I've noticed that there aren't really any OFFICIAL list of ALL the places that accept ApplePay, and since I'm a huge fan of the service/thing I decided to keep a list of places I have found that accept the technology.
Fairway (Grocery chain in New York)
New York TaxiCabs (TLC)
Union Market (Houston Street)
Push Cart Coffee (on 25th and 9th)
CitiBike (new stations will enable you to unlock with ApplePay)
aside from all the obvious ones: