The incident was reported just after 6 a.m. on Dec. 5 at the store store at 686 10th Avenue.
Surveillance video shows the two suspects walk into the store before one held a gun to the teen and forced him to empty the register.
The suspects ran away northbound on 10th Avenue with about $100.
The 17-year-old employee was not injured.
Anyone with information is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).
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