The incident happened on West 83rd Street off Amsterdam Avenue after 10:30 a.m.
The iron workers were doing renovations on the building when they fell down the shaft, investigators said.
The beam they were working on gave way, officials said. They fell seven floors, about 60 feet.
Rescue crews rushed both men to area hospitals where both were pronounced dead.
The victims were a 49-year-old Brett McEnroe of Dover Plains and a 51-year-old Roy Powell of New Paltz.
The site has had a dozen violations over the past four years, including a currently active violation for failing an annual elevator inspection test in October. Today's accident occurred near the external elevator.
The site also has 10 open Environmental Control Board violations. In May, the Environmental Control Board issued a violation notice for failure to secure scaffolding.
The contractors, F. J. Sciame Construction Co. Inc., said the two workers were employed by Weir Welding and Cross County Erectors.
"Sciame Construction Co. Inc. is fully cooperating with the investigation and extends its deepest sympathy to the families of the men who lost their lives today," the company said in a statement.
Redeemer Presbyterian Church purchased the building on West 83rd Street for $21.5 million in 2009, according to city records.
A church plans to turn it into a community center and worship space