The governor said the decision hasn't changed anything and called the court's action "irrelevant from any practical impact."
However, leaders of the two groups who are plaintiffs in the case — the Roman Catholic Diocese of Brooklyn and Agudath Israel, an advocacy group for the Orthodox Jewish community — disagreed, saying that the case about religious liberty and more sensible health measures.
Cuomo, for his part, pointed out that the Catholic church and Orthodox Jewish synagogues in Brooklyn and Queens are no longer subject to them.
"I think this was really just an opportunity for the court to express its philosophy and politics," Cuomo said.
The justices split 5-4 on the decision, with new conservative Justice Amy Coney Barrett representing the decisive vote in the majority. It was Barrett's first publicly discernible vote as a justice.
The court's three liberal justices and Chief Justice John Roberts dissented.
In an unsigned order, a majority of the court said New York's restrictions "single out houses of worship for especially harsh treatment."
Bishop Nicholas DiMarzio of the Brooklyn Diocese said that the ruling is relevant far beyond the boundaries of the New York City region.
"There are places where, for example, I'm on the board of the National Shrine of the Immaculate Conception in Washington D.C.," DiMarzio said. "That church seats 5,000 people. They are only allowed to have 100 people, by the laws of the District of Columbia."
"The district refused to hear their plea," he said. "We have the same problem."
Rabbi Chaim Dovid Zweibel is the executive vice president of Agudath Israel.
"It made no sense to treat a small synagogue that seats 25 people on a regular basis the same as a synagogue that seats 500 people," he said.
For Cuomo, it came down to public safety.
"I fully respect religion, and if there's a time in life we need it, the time is now," Cuomo said. "But we want to make sure we keep people safe at the same time."
Cuomo said the Supreme Court is "different" now, referencing Coney Barrett tipping the court more towards conservatives.
Earlier in this year, when Barrett's liberal predecessor, Justice Ruth Bader Ginsburg, was on the court, the justices divided 5-4 to leave in place similar pandemic-related capacity restrictions affecting churches in California and Nevada.
Two lower courts had sided with New York in allowing the restrictions on houses of worship to stand.
The governor asserted that the Supreme Court decision isn't final, saying that it would go back to the Second Circuit Court of Appeals.
When asked by a reporter if he felt the ruling would convince churches and synagogues they now have the leeway to host gatherings of thousands, Cuomo disagreed.
"It didn't affect our mass gathering rules...It didn't mention the overall limits," he said.
President Donald Trump seemingly celebrated the court's decision on Twitter Thursday morning, writing simply "Happy Thanksgiving!" while sharing a tweet of the news from the @SCOTUSblog account.
During Trump's single term in office, he appointed three of the justices sitting on the Supreme Court, including Barrett. Conservatives now have a 6-3 majority.
This story was originally published by Jay Dow, James Ford and Mark Sundstrom on WPIX in New York City. The Associated Press contributed to this report.