The 27-year-old actress donned a long teal wig, black sweatpants and a tank top during her brief appearance.
Manhattan prosecutors filed an affidavit from her building manager, Rudy Toro, corroborating police and prosecutors' account of the incident. Bynes' next court appearance was scheduled for Sept. 26.
Back in May, Bynes was arrested after building officials called police to complain that Bynes was rolling a joint and smoking marijuana in the lobby.
Officers went up to her apartment, where they said they saw heavy smoke and a bong sitting on the kitchen counter. They said the actress tossed the bong out the window in front of them, according to prosecutors.
After her first court appearance, where she wore a disheveled blond wig, she accused the officers who arrested her of sexual assault; police are looking into her claims. She also has taken to social media to criticize a host of celebrities recently.
Bynes had no previous arrests in New York, but she was involved in several cases in California. In December, she resolved a misdemeanor hit-and-run case after entering into a settlement with other drivers.
Also, she was charged last fall with driving on a suspended license after it was temporarily taken away from her following two hit-and-run cases where she was accused of leaving the scene without providing proper information. She has also pleaded not guilty to drunken driving in a separate case.
It's not clear how the New York case will affect the California ones.
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.