139 were removed on the first night, Mayor Bill de Blasio said.
"That's an extraordinary number for one night and very encouraging," he said. "More than half of the people encountered and engaged, agreed to leave the subways to leave the streets and come in and that's an amazing reality to begin with. But we have more importantly never ever seen so much success in a single night before."
The subway system went silent from 1 to 5 a.m. Wednesday as part of a plan for the normally round-the-clock system to shut down for train cleaning.
The NYPD's Homeless Outreach unit and other social workers offered to trade a subway bench inside the World Trade Center E train station for temporary shelter.
Cleaners carrying bottles of bleach then boarded the trains.
The New York Police Department has assigned more than 1,000 officers to secure many of the system's 472 stations, as fewer than 200 can be physically locked up.
Outreach teams made up of officers and nurses are being sent to 29 end-of-line stations to roust homeless people from trains as they are taken out of service.
New York City normally has the country's busiest public transit system, with a weekday ridership of more than 5 million. But ridership has dropped more than 90% during the pandemic.
More information is available from the MTA at new.mta.info/coronavirus/overnight.
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