The suspect, 43-year-old Kevin Canty, retired from the force about a year ago.
He faced a judge Sunday night, charged with second-degree murder and criminal use of a firearm.
Authorities say he shot 40-year-old Jessica Canty in front of the couple's two small children, ages 4 and 7, on Saturday morning in Ozone Park.
Neighbors say they heard several gunshots coming from inside the house, then saw the two kids come running out of their home screaming that their father had shot their mommy.
"Once I heard the shots, I jumped up and saw the babies in the street," neighbor Lisa Santiago said. "They were in the street screaming 'please, please help!' They were banging on the cars."
Some area residents ushered the children to a nearby store and called police.
"The kids were hysterical," neighbor Heidi Gamble said. "'Please help my mom, help my mom. My dad shot my mom, and there's blood all over the wall.'"
Officers responded to the scene at 11 a.m. and found the victim with multiple gunshot wounds to her stomach. She was rushed to Jamaica Hospital, where she was declared dead.
Police say Kevin Canty had fled the scene, and an intense manhunt followed, involving a SWAT team and NYPD officers. He was allegedly intoxicated when he was found.
"They had the helicopters flying around, and had the SWAT team around," neighbor Vincent Eccleston said. "They didn't know where he was."
Canty became an officer in December 1994. Neighbors say the couple had a troubled marriage, but the events leading up to the shooting are unknown.