Eyewitness News is told the threats were made via email to the building on Eastern Parkway in Crown Heights.
"An email, saying that there were three pipe bombs in the museum that would go off some time today," museum director Devorah Halberstan said.
New York Governor Andrew Cuomo's office sent a tweet that the governor was briefed at the scene.
"This is one of the cruelest ironies yet in this rash of anti-Semitism that we've been experiencing," Cuomo said. "This is a museum that is a monument to tolerance."
The building was evacuated as a precaution, but the museum was not yet open.
"It's immoral, it's unethical and it's also illegal," Cuomo said. "And we are going to find the people who are doing these threats."
The Jewish Children's Museum is the largest Jewish themed Children's Museum in the United States. It was built back in 2005, and its Halberstan is the mother of 16-year-old Arie Halberstam, who was murdered on the Brooklyn Bridge by a Lebanese gunman in 1994.
"This is very painful to me," Devorah Halberstam said. "Very, very painful to me. I feel like I'm kind of reliving my son's murder."
And yet, moments after authorities cleared the building, parents and their young children were determined to come see the sights, in an effort not to show fear in the face of these threats.
"The person who did this must be a very sad person," visitor Shelley Hoffman said. "A person who doesn't believe in personal freedom for everybody."
Amid a sharp increase in threats made to Jewish institutions and the Anti-Defamation League, the NYPD is advising a measured response in most cases, including conducting searches rather than immediately evacuating an entire building.
They say the evacuation and fear it instills is considered a payoff to the threat, but all precautions should still be taken on a case-by-case basis.
The investigation is ongoing, and anyone with information is urged to contact police.