The incident happened at Wyandanch Beer Co. on Long Island Avenue in Suffolk County around 3:30 p.m. Saturday.
Surveillance video shows one of the men moves a smaller jar out of the way while the other man grabbed a larger jar and put it under his hoodie.
The donations, which totaled between $30 and $40, were meant to help a 12-year-old girl with a life-threatening disability.
The suspect was described as a heavy-set, dark-skinned black male, approximately 5 feet 10 inches tall.
Anyone with information is asked to call police.