The incident happened at the Whole Foods on East Houston and Bowery around 10 p.m. Sunday night.
Authorities say approached a group of employees who were transporting $60,000 from the first floor via the elevator to the second floor.
The suspects waited by the elevator on the second floor, and when the door opened, one of them displayed a handgun.
The second suspect grabbed one of the employees and tied his hands behind his back before both suspects fled the store with the money onto Chrystie Street.
The first suspect is described as a black male about 6-feet tall with black eyes and black dreadlocks wearing brown coat.
The second suspect, also a black male, had dreadlocks and was wearing black sweater.
Anyone with information in regards to this incident is asked to call Crime Stoppers at 1-800-577-tips (8477).