Among the first out were 20 babies in neonatal intensive care, some on battery-powered respirators.
"Everyone here is a hero," Dr. Bernard Birnbaum, a senior vice president at Tisch Hospital, the flagship at NYU, told exhausted crews as he released all but essential employees late Tuesday morning. "Thank you, thank you, thank you."
More than two dozen ambulances from around the city lined up around the lower Manhattan block to transport the sick to Mount Sinai Hospital, the Memorial Sloan-Kettering Cancer Center, St. Luke's Hospital, New York Presbyterian/Weill Cornell Medical Center and Long Island Jewish Hospital.
Margaret Chu, 36, of Manhattan, gave birth to a son, Cole, shortly before noon Monday.
"Then, a couple of hours later, things got a little hairy. The electricity started to flicker and the windows got shaky," she said from LIJ's Lenox Hill, where she was transported after generators failed and NYU was plunged into darkness.
Chu, accompanied by husband Gregory Prata, was able to walk 13 flights into a waiting ambulance with help from staff and first responders lighting the way by flashlight. She said other women who had given birth during the storm were carried down on sleigh-like gurneys.
"Everybody was pretty calm. I would call it organized chaos," she said.
Meanwhile, other New York hospitals canceled outpatient appointments and elective surgeries. And several closed and evacuated patients, including New York Downtown Hospital, a Manhattan campus of the VA New York Harbor Healthcare System and other NYU-affiliated facilities. Coney Island Hospital was evacuating Tuesday afternoon.
Mayor Michael Bloomberg was clearly angry about the NYU Medical Center crisis when he addressed reporters late Monday, saying hospital officials had assured the city they had working backup power.
Last year, NYU evacuated in advance of Hurricane Irene on the order of city officials, spokeswoman Allison Clair said. "This year we were not told to evacuate by the city."
Without power, there are no elevators so patients -- some of whom were being treated for cancer and other serious illnesses -- were carefully carried down staircases. As the evacuation began, gusts of wind blew their blankets while nurses and other staff huddled around the sick on gurneys, some holding IVs and other equipment.
Luz Martinez, 42, of Roosevelt Island off midtown Manhattan in the East River, was home recuperating from a cesarean section when she got her first inkling that her 3-week-old daughter was being transferred out of NYU's neonatal intensive care.
The baby, Emma, had been born prematurely. Martinez had been calling the hospital for regular updates but at one point Monday night, the phones were busy every time she called. Then she heard Bloomberg on television talking about the evacuation and soon after lost power at home.
"I went crazy. I wanted to come to the hospital," Martinez said.
She and her husband hopped in the car but could find no way into Manhattan because of storm damage and bridge closings. That's when NYU called her on her cellphone to say Emma was being taken to Mount Sinai.
But the terrified parents couldn't get there, either. They called Mount Sinai through the wee hours for regular updates and finally reached their baby around noon Tuesday.
"It was a nightmare," Martinez said by phone. "I've been doing a lot of crying."
Emma is doing fine. Martinez praised the staff at both hospitals. "They all handled everything as smoothly as they could," she said.
NYU sent home about 100 of its 400 patients earlier Monday to lighten its load, starting the evacuation of the remaining 300 patients at about 7:30 p.m. when backup generators began to fail, Clair said. There were no injuries during relocation.
The scene was reminiscent of hospital evacuations in New Orleans after Katrina, with patients being carried down stairs on stretchers because elevators were out, and nurses squeezing oxygen bags for them because of lack of power to run breathing machines.
The difference is that in New Orleans, patients were trapped in flooded hospitals; in New York, dozens of ambulances could get through to move patients to safety.
The hospital blamed the severity of Sandy and higher-than-expected storm surge that flooded its basement but had little else to say beyond a short statement emailed to reporters after the evacuation was complete.
"At this time, we are focusing on assessing the full extent of the storm's impact on all of our patient care, research and education facilities," the statement said.
Most of the power outages in lower Manhattan, where Tisch is located, were due to an explosion at an electrical substation, Consolidated Edison said. It wasn't clear whether flooding or flying debris caused the explosion, said John Miksad, senior vice president for electric operations at Con Edison.
At NYU, sporadic telephone service made it difficult for the hospital to notify relatives where patients were taken. It relied instead on receiving hospitals to notify families.
Until the generators failed, Chu considered herself and her new baby out of harm's way. By the time she was evacuated, the streets were eerily silent and the night sky lit up by emergency lights of waiting ambulances.
"My son will appreciate this someday," she said.