The 27-year-old appeared disheveled in a long blond wig and sweat pants on Friday in a criminal court, where she was charged with reckless endangerment.
The incident happened at an apartment building on West 47th Street at about 7:40 p.m. Thursday.
Police arrived at the building after a doorman called to complain that Bynes was smoking marijuana and rolling a joint in the lobby.
Officers say they went to Bynes' apartment on the 36th floor and saw heavy smoke and a bong sitting on the kitchen counter. Authorities say she tossed the bong out of the window in front of them.
She then said to police: "It was just a vase," according to Manhattan assistant district attorney Chikaelo Ibeabuchi.
"My client completely denies illegally throwing anything out of her window," said Andrew Friedman, her attorney for the arraignment.
Bynes was arrested on charges of reckless endangerment, tampering with evidence and criminal possession of marijuana. Thursday, she was held overnight at a police precinct.
The judge released Bynes on her own recognizance and gave her a July 9 court date. He warned the actress that failing to appear or being late for future court appearances would be costly.
Bynes rose to fame starring in Nickelodeon's "All That" and has also starred in several films, including 2010's "Easy A." But she has been in the news more recently because of several scrapes with the law and bizarre public behavior.
The Associated Press contributed to this report.