As many as three suspects are in custody, according to police.
The two officers, one male and one female, were on a patrol in a housing complex in the South Bronx when they and another officer encountered two men in a stairwell, First Deputy Commissioner Benjamin Tucker told reporters.
One of the men in the stairwell fired at the officers and fled to an apartment of an acquaintance.
Giselle Cruz, who lives directly across the street, told CNN she heard five or six gunshots.
According to the Chief Edward Mullen, a male officer, 29, was shot in the face. A female officer, 24, was shot in the stomach.
NYPD didn't identify the officers, who each have been on the force for two years. Police also didn't identify the dead gunman.
Mayor Bill de Blasio called the officers "brave."
"So far, in both cases, their condition is good," he said. "I'm pleased to say both officers have been alert and communicating."
NYPD tweeted the officers' conditions were stable.
Responding officers found the suspect dead in an apartment where a .32-caliber pistol and a shotgun were recovered.
Police are interviewing four other people, including the other person who was in the stairwell.