Police say the 12-year-old boy was approached by a man in the second floor men's room at around 7:30 p.m.
The boy was allegedly lured into a stall by the suspect and then allegedly sexually assaulted.
He resumed shopping with his grandmother only told her about 90 minutes later, prompting a police investigation.
He was evaluated at Bellevue Hospital.
The suspect is described as male age 30-45, 5'7"-5'9", with a medium complexion, brown and gray hair with facial hair.
He was last seen wearing a white shirt and grey sweatpants.
Anyone with information in regards to this incident is asked to call the NYPD's Crime Stoppers Hotline at 800-577-TIPS.