Employees of the store at 95 East Houston St. were moving the money in an elevator from the first to the second floor about 10 p.m., police said.
As the elevator doors opened, one of two thieves pointed a silver gun at the employees and ordered them to the ground while the other man bound one of workers, police said.
The men snatched the money and fled south on Chrystie Street, the NYPD said.
The gunman is described as about 6-feet-tall, had dreadlocks and wore a brown coat, police said.
His partner also had dreadlocks and wore a black sweater, police said. Both were caught on security cameras.
No injuries were reported in the incident, an NYPD spokesman said.
Anyone with information is asked to call Crime Stoppers at (800) 577-TIPS (8477).