I don't recall getting stickers at any clubs NYC, although it's been a few years since I lived there. It was always on the honor system at places like Output and events like Black Market.
Maybe it varied depending on the night, but I remember Output being stricter about it the first few years they were open – staff would regularly confront people who took photos. But that seemed to fall off entirely over their final couple years.
Output was definitely doing stickers for a while, I still have several of them (on a stickerbombed bicycle frame). I can't remember whether that was in the early years or the late years though.