Thirty-six-year-old officer Rosa Rodriguez is at Weill Cornell Medical Center, while 38-year-old officer Dennis Guerra is being treated at Jacobi Medical Center in the Bronx.
Three firefighters and two people in the building were treated for minor injuries.
A 16-year-old boy who lives in the building was taken into custody, and arson investigators are building their case.
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The fire at 2007 Surf Avenue started with a mattress burning in the hallway on the 13th floor, and the two officers responded in less than a minute.
"It was really smokey, and you couldn't breathe," one resident said. "And it was coming into the house."
As residents fled, the officers took the elevator to help people get out.
"As soon as the elevator door opened, they were overcome by the smoke that in the hallway," NYPD Commissioner William Bratton said. "They were on the floor of the hallway when responding firefighters got there."
The officers were overcome in just moments, suffering smoke inhalation and carbon monoxide poisoning
"Today is another sobering reminder of the dangers that face all of our first responders, certainly the men and women of the NYPD," Mayor Bill de Blasio said. "Two very brave officers."
Guerra was airlifted to Jacobi from Coney Island Hospital. He was resuscitated in the field. Rodriguez was moved from Lutheran Hospital to Weill Cornell to be treated for a burned esophagus inside the hospital's hyperbaric chamber.
"Having been first stabilized at Coney Island Hospital and Lutheran Medical Center, where they did a phenomenal job, they were transferred to these other hospitals because of specialized capabilities there and their burn units," NYPD Chief Surgeon Dr. Eli Kleinman said.
Both Guerra and Rodriguez have four children. Rodriguez has been on the force for three years, and Guerra for seven.
The teenager remains in custody, but so far, no charges have been filed. He reportedlytold detectives that he set the mattress on fire with a lighter because he was bored and wanted excitement, but he was then unable to put it out. He banged on a couple doors and ran out of the building with other residents. He told detectives he was trying to get people out.
Sources say the teen has set at least one fire before. He has an arrest for arson in 2010 and other prior arrests as a juvenile.