The incident was first reported on Saturday around 3 a.m. at the site on Christopher Street in Greenwich Village.
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Photos show the flags broken and sprawled on the ground.
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The NYPD released surveillance video of three people they are looking for in the case.
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Authorities say they fled the scene on foot.
The NYPD 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). The public can also submit their tips by logging onto the Crime Stoppers website at https://crimestoppers.nypdonline.org/, on Twitter @NYPDTips.