It happened sometime overnight Sunday at La Nacional on West 183rd Street in the University Heights section.
Police say the suspect first broke through the back wall of a neighboring business, Del Valle Fruit & Vegetables, before entering La Nacional through the ceiling.
More than $66,000 was stolen from two safes and two registers.
The theft was discovered on Memorial Day.
Anyone with information in regard to this incident 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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