Luis Ramirez had been stopped earlier on his road trip in Kansas City where police discovered a firearm, according to police sources.
He had no weapons when the Port Authority Police stopped him on Friday, officials said.
The online threats were made in a social media post. An earlier post referenced Central Synagogue on Lexington Avenue.
Ramirez is being held at the Hudson County jail in Kearny.
Mitch Silber, executive director of UJA's Community Security Initiative, said these instances against the Jewish community are far too common.
"Unfortunately, this incident underscores that Jewish communities around the world and even here in New York are under threat in 2025 and now require dedicated Jewish security organizations to keep them safe," he said.
"What began as a terrible anomaly in Pittsburgh in 2018 at Tree of Life Synagogue with an attack targeting a Jewish house of worship, has become a regular facet of Jewish life in America."
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