The bodies were found on Sunday, but no identities have been released.
Two people have been reported missing from a sushi restaurant hit by the blast: Nicholas Figueroa, who was on a date there, and a worker, Moises Lucon.
A further 22 people were injured in the explosion and subsequent fire, four critically.
Utility inspectors had declared plumbing and gas work inside one of the buildings faulty just an hour before the explosion, locking the line to ensure it would not be used and then leaving, officials said.
The blast that followed soon after left heaps of bricks and mangled debris across the street in Manhattan's East Village.
Mr Figueroa's date, who is being treated in hospital, remembers only stumbling out of the restaurant before losing consciousness.
New York Mayor Bill de Blasio said officials would investigate whether anyone had improperly tapped the gas supply prior to the blast.
Two bodies been found at the site of a massive gas explosion that flattened three buildings in New York on Thursday.