The USNS Comfort has been docked at Pier 90 on the west side of Manhattan for three weeks, but soon it will leave and head back to Virginia.
The navy hospital ship's arrival was celebrated, but the medical staff on board have treated few patients.
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Cuomo also says Trump agreed to help New York state aggressively expand its testing capacity in the coming weeks with states handling logistics and the federal government helping secure supplies.
"The federal government will work along with the state on the national manufacturers and distributors together, we'll all work together," Trump said.
"That is an intelligent division of labor in my opinion, let each level of government do what it does best," Cuomo said.
Eventually the governor wants to be able to double the testing capacity from 20,000 40,000 people a day.
He says knowing who has the virus and who has recovered is the key to reopening the economy.