The fury started when the governor told a local radio station on Monday afternoon that he planned to spend the holiday with his mother and daughters.
"My mom is going to come up and two of my girls is the current plan. But the plans change. But that's my plan," he said.
His plans sparked criticism on social media. Detractors called Mr Cuomo a hypocrite for asking New Yorkers to cancel their family gatherings while he still planned to have his.
Christopher Ingraham, a Washington Post reporter, chastised Mr Cuomo for not leading by example.
"Un-freaking-believable. Now more than ever, people are looking to elected leaders for signals on how to mitigate risk. Is it any wonder so many aren't following health guidelines? And this is the allegedly pro-science party!" he wrote.
Shortly after the blowback, Mr Cuomo's senior adviser confirmed that the governor would be working through the holiday, and his family plans had been cancelled.
"As the Governor said, 'The story is my mom is going to come up and two of my girls is the current plan, but the plans change. That's my plan. I'm going to work — I've got a lot of work to do between now and Thanksgiving,' and given the current circumstances with COVID, he will have to work through Thanksgiving and will not be seeing them," senior adviser Rich Azzopardi said.
New York, like the rest of the country, has experienced a spike in coronavirus cases in recent weeks. The number of hospitalisations in the state has doubled since the first week of November, and more than 26,000 people have died.
Mr Cuomo has previously suggested that people who get infected with the virus bring it on themselves by not following health guidelines.
“So, the restrictions work and just to make it very simple: If you socially distanced and you wore a mask and you were smart, none of this would be a problem. It’s all self-imposed. It’s all self-imposed,” Mr Cuomo said.
“If you didn’t eat the cheesecake, you wouldn't have a weight problem.”
Mr Cuomo is not the only East Coast governor taking heat for hypocrisy ahead of Thanksgiving.
The women who were filming the encounter with the Democratic governor harassed him and called him "such a d****."
Though Gov. Murphy did not address the women at the time of the encounter, he later spoke out and said eating outside with his immediate family was not a violation of the orders he gave advising people not to meet in large groups for Thanksgiving.
“There’s no reason we should have to be having a political discussion about whether or not you’re wearing a mask. We were dining outdoors in the middle of our meal," he told CBS This Morning.
"I’d prefer folks to be more civil and to leave our kids out of this."
On 25 November, Mr Murphy is expected to place the city of Newark on a ten-day lockdown during which residents will be asked to leave their homes only for emergencies.