ESU Detective Hassan Hamdy was charged with "failing to employ proper tactics causing a civilian's death" in the shooting that killed 22-year-old National Guardsman Noel Polanco.
Sergeant Thomas Glaudino will also receive departmental charges for failing to supervise Hamdy. Glaudino was in charge of the unit that made the stop.
Polanco was shot in the chest after he was stopped for reckless driving on the Grand Central Parkway on October 4, 2012.
A Queens grand jury declined to indict Hamdy, but the city agreed to pay a $2.5 million settlement to Polanco's family in February.
Hamdy could be terminated if found guilty in an NYPD departmental trial.
The head of the Sergeants Benevolent Association, which represents Glaudino, called it a "typical scapegoat reaction by the department, second-guessing what happened."
Polanco's mother, Cedilia Reyes, has been advocating for Hamdy to be removed from the force. In February, she appeared at the National Action Network to say the detective should not be working in law enforcement.