It also received a threat on the morning of January 31, when an automated phone call about a bomb prompted the evacuation of the facility.
New York City's head of police intelligence said Thursday that investigators believe one man using a voice changer and phone spoofing device is behind a large number of the scores of threats made against U.S. Jewish institutions this year. The NYPD evacuated everyone from the building and barred people from entering as officers inspected the museum.
She spoke outside the museum Thursday alongside Gov. Andrew Cuomo, and broke down as she was reminded of her son and the message of tolerance the museum stands for.
In a letter to Jeff Sessions, the JCC Association of North America expressed appreciation for Trump's condemnation of anti-Semitism, but expressed frustration with the speed of progress in countering bomb threats.
At about 10 a.m., the museum posted to its Facebook page that it would be closed until further notice.
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It would not be the first to decide not to run it - a drive-in theater in Alabama already made that call. A Russian law enacted in 2013 prohibits the spread of " gay propaganda " to minors.
The gunman, a Lebanese immigrant, killed 16-year-old Ari Halberstam in 1994.
"We call upon our public officials, at every level of government, to speak out about these events and all hate crimes, and do everything in their power to put a stop to these threats and incidents", council Chairman Harvey Wolbransky said.
Officials swept the space, and no explosives were found. Police officials said two Jewish community centers in upstate NY were also evacuated and shut down after bomb threats were phoned in.
The threat comes of the heels of several others against Jewish gathering places and institutions around the city over the past few weeks.
This is a developing story.