"It wasn't always easy, but students, educators and parents stepped up to fight this pandemic," Hochul tweeted on Sunday. "We've reached this exciting milestone because of your hard work."
The new rules come after the U.S. Centers for Disease Control and Prevention on Friday eased guidelines for indoor masking across most of the country.
The CDC's latest school guidance recommends masking only in areas of high Covid-19 transmission, instead of universal masking.
New York's positive test rate on a seven-day rolling average was 1.9 percent on Friday, according to the state health department website, down from over 20 percent in early January.
Counties and cities may still require masks to be worn in schools. New York City Mayor Eric Adams said on Sunday the city would lift its school mask mandate on March 7 if there are no "unforeseen spikes" in Covid-19 cases between now and Friday.
"Our schools have been among the safest places for our children since the beginning of the pandemic, and we will continue to make the proper public health decisions to keep our kids safe, including making masks available for any child or school staff member who wishes to continue wearing them," Adams said in a statement.