Authorities said they received an emergency call reporting two jumpers from the 52-floor building on the Upper West Side around noon. Officers responding to the scene found the 35-year-old man and the boy on the rooftops of two separate nearby buildings.
The man was pronounced dead at the scene and the child was pronounced dead at a nearby hospital, police said. No identifications were released.
The circumstances of the fall are unclear. Authorities said the father did not appear to live in the building.
Luis Ortiz told the New York Post that he was at the hospital when paramedics rushed the boy there and that they were pumping his chest and working on him.
"You could tell he was slipping away. They said the father was up there, but they didn't bring anyone else in. It was just heartbreaking. I have two kids of my own. They tried to do the best they could," Ortiz told the newspaper.
Police investigating the deaths left the building in the mid-afternoon to photograph a gray Lexus RX350 parked nearby.
The building, listed as South Park Tower, is a short distance away from Columbus Circle and Lincoln Center.
In March, a woman clutching her baby son in her arms plunged eight stories out of a Harlem apartment window to her death, but the 10-month-old survived. Authorities found a suicide note in her home.