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A Buzzfeed News report said the group, including those dressed in yarmulkes, met the Republican on Thursday morning outside an elevator.
A witness said Ms Boebert looked at the group “head to toe” and then asked them if they were there for “reconnaissance”.
“When I heard that, I actually turned to the person standing next to me and asked, ‘Did you just hear that?’” said a rabbi who was with the group.
“You know, I’m not sure [whether] to be offended or not. I was very confused,” he added.
Ms Boebert said she was cracking a joke that referred to reports that she had given a tour of the Capitol building to a large group just days before last year’s insurrection.
She added that some people in the group “got it”.
“I saw a large group and made a joke. Sadly when Democrats see the same they demonise my family for a year straight,” she said.
“I’m too short to see anyone’s yarmulkes.”
The group was visiting representative Tom Suozzi who had brought them to commemorate the 41st anniversary of the Iran hostage crisis.
“The bottom line is that everyone, especially members of Congress, have to be very, very thoughtful in the language they use,” Mr Suozzi said in a statement.
“Because when you’re a member of Congress, you have an important role to play in society.”
“You can’t be cavalier in the comments you make especially if they could be perceived as being antisemitic, or discriminatory,” he added.
Ms Boebert, known for her gun advocacy and opposition to Covid restrictions and mandates, faced backlash last year for her comments against her colleague Ilhan Omar.
The comments were widely condemned as racist and Islamophobic.
The Colorado Congresswoman was recently made communications chair for the House Freedom Caucus.