Officers responding to an emergency call reporting two jumpers from the building on the Upper West Side around noon Sunday found Dmitriy Kanarikov, 35, of Brooklyn, and the boy on the lower rooftops of two separate nearby buildings.
The man was pronounced dead at the scene and his son, Kirill Kanarikov, was pronounced dead at a nearby hospital, police said.
The boy's mother had custody of the child and the father, who had visiting rights, was supposed to hand the boy over to the mother at a police precinct Sunday afternoon, authorities said.
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.
Authorities said the father did not live in the building listed as South Park Tower, which is a short distance away from Columbus Circle and Lincoln Center.
Police investigating the deaths left the building in the mid-afternoon to photograph a gray Lexus RX350 parked nearby.
It's the second time this year that a parent and child have been involved in a fatal plunge from a New York apartment building.
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.
Associated Press writer Tom McElroy contributed to this story.
