Yoselyn Ortega - lying handcuffed in her hospital bed in silence, her right hand trembling - entered the plea through her defense attorney.
"I ask you to enter a not guilty plea on behalf of my client," said the lawyer, Valerie Van Leer-Greenberg.
Van Leer-Greenberg also told Judge Lewis Bart Stone that her client remains "profoundly, medically impaired and in need of medical attention."
Stone ordered Ortega held without bail while she undergoes psychiatric exam. The judge, like two prosecutors and everyone else crowded into the room, wore a hospital gown.
Ortega, 50, appeared alert but didn't speak during the 10-minute hearing.
She had a tube leading to her throat, but was breathing on her own. She wore a blue hair net. No wounds were visible.
The hospital room was sparse: There were no flowers, photos or other personal items on display.
The unusual bed-side arraignment came as District Attorney Cyrus Vance Jr. announced an indictment charging Ortega with multiple counts of murder.
"This crime shocked and horrified parents around the city, many of whom entrust their children to the care of others both by necessity and by choice," Vance said in a statement.
"My heart goes out to the family of those beautiful young children, and I hope that, with time, this family will heal."
Van Leer-Greenberg left the hospital without speaking to reporters.
Authorities allege that on the evening of October 25, while the children's mother was out with a third child, Ortega repeatedly stabbed 6-year-old Lucia Krim and her 2-year-old brother, Leo.
When their mother, Marina Krim, returned with her 3-year-old daughter, she found their bodies in the bathtub, with Ortega lying on the bathroom floor with stab wounds to her neck. A kitchen knife was nearby.
The children's father, CNBC digital media executive Kevin Krim, had been away on a business trip when the killings occurred.
The couple's apartment building sits in one of the city's most idyllic neighborhoods, a block from Central Park, near the Museum of Natural History and blocks from Lincoln Center for the Performing Arts. The neighborhood is home to many affluent families, and seeing children accompanied by nannies is an everyday part of life there.
Some of Ortega's friends and relatives said she appeared to be struggling emotionally and financially recently, but they still couldn't believe she could have committed such a heinous act.