The vote overrode Mayor Michael Bloomberg's veto and prompted him to claim that the city's safety was being jeopardised.
New York Police Department has come under scrutiny for its heavy use of stop and search tactics and its extensive surveillance of Muslims.
The vote comes less than two weeks after US District Court Judge Shira Scheindlin ordered monitoring to focus on stop and search.
She said the practice had violated the rights of hundreds of thousands of black and Hispanic men.
Civil rights groups have been pushing for the legislation.