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Witnesses described a chaotic scene. "They shot her and pulled her out of the car. Then she started screaming," said Ayanna Blackman, 38, who watched from her apartment on the same corner.
Witnesses said the woman was covered in blood when she was pulled from the car.
Two elected officials from the area, Assemblyman Nick Perry and Councilmember Jumaane Williams, appeared on the scene and called for an investigation into the shooting.
A crowd gathered in the tense hour after the incident, and shouts of "murderers" were directed at police officials on the scene.
The shooting comes at a time of heightened public scrutiny of the NYPD's tactics, particularly in some of the city's minority communities.
A narcotics-enforcement officer pleaded not guilty to manslaughter charges Wednesday in the fatal shooting in February of an unarmed African-American teenager in the Bronx. Officer Richard Haste was the first officer to be charged criminally in an on-duty shooting since three officers were indicted in the 2006 death of Sean Bell.