"We must have zero tolerance for any abuse or discrimination of any fellow human being," Cuomo said at the end of a tour at the 'Yad Vashem' museum in Jerusalem.
"It is disgusting, it is reprehensible, it violates every tenant of the New York state tradition," he said.
Israeli President Reuven Rivlin, who accompanied the governor, said: "Jews must be safe wherever they are, wherever they are in the world, especially and specifically in the United States."
Cuomo's visit came only hours after reports of another act of vandalism at a Jewish cemetery in Brooklyn, New York.
It said that several headstones were knocked over, and the NYPD was investigating.
It was the fourth known case of a Jewish cemetery desecration in the US in the past two weeks, but it was yet to be known whether it was motivated by antisemitism.
Cuomo said on Thursday that he had ordered the investigation of the vandalism of more than a dozen headstones at a Jewish cemetery in Rochester, New York, given the wave of bomb threats that later proved hoaxes targeting Jewish community centers and vandalism at Jewish cemeteries in Philadelphia and St. Louis.
US President Donald Trump, a Republican, has condemned the threats and attacks, although he has at times also questioned whether some perpetrators might be his opponents seeking to link his new presidency with a rise in antisemitism.
Trump's election campaign last year drew support from some white nationalists and right-wing groups, despite his disavowals of them.
During their visit at Yad Vashem, Cuomo and Rivlin toured the museum, laid a wreath and lit the 'Eternal Fire' during a ceremony at the Hall of Remembrance.