The incident happened Nov. 10 at Bagels and Company on Union Turnpike in Fresh Meadows.
Police say the suspect was recording on his phone when he told one of the store's employees to remove Israeli flags hanging at the shop.
He also told them to shut the business down or he would burn down the building.
"No acts of anti-Semitism or hate of any kind will ever be acceptable in this community," said New York State Assembly member David Weprin. "We must strive to embody and at times defend the spirit of welcome and acceptance."
Two men who confronted the suspect were honored for their bravery.
Police are still searching for the man who made the threats. The NYPD's Hate Crimes Task Force is investigating.
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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