Waters joined the British drummer at the Beacon Theatre for a rendition of "Set the Controls for the Heart of the Sun", from the band's 1968 album "A Saucerful of Secrets".
Mason has been on a North American tour with his group, Nick Mason's Saucerful of Secrets, since early March, performing some of Pink Floyd's early material.
The band consists of Spandau Ballet's Gary Kemp, Lee Harris of Ian Dury & The Blockheads, composer Dom Beken and former post-Waters Floyd bassist Guy Pratt.
According to BrooklynVegan, Waters told the group: "You guys sound better than we did back then," and even returned after the encore to take a bow with the musicians.
The get-together comes months after Mason told fans at a London show in September (2018) that he had "finally given up waiting for that phone call" for another Pink Floyd reunion with Waters and David Gilmour.
They last performed together at Live 8 in London's Hyde Park on July 2, 2005. Keyboardist Rick Wright died in September, 2008.