CEO Janno Lieber said the MTA had service restored on all but one of its lines within a day of the historic storm.
He insists the subway system worked as designed and is trusted by commuters.
Subways struggled to return following widespread flooding from Ida.
The 4, 6, E, F, and N lines were partially suspended, and the 1, 2, 3, 5, 7, A, D, M, G, J, L, Q and R lines experienced delays due to residual damage.
Lieber also said subways broke a coronavirus pandemic ridership record Tuesday with 2.9 million commuters.
That's 150,000 more riders than on the previous record-setting day on Monday.
"The system is safe, 70% of our workforce is vaccinated, mask usage remains high, and our subways have much better ventilation systems than restaurants and offices," Lieber said.
Lieber said riders are returning to a much-improved system, which includes the new 42nd Street shuttle.
He said the MTA is also hiring more staffers and training employees to keep service fast and reliable.
But despite those reassurances, the MTA workforce has one of the lowest vaccination rates among public employees in New York. Nearly 30,000 transit workers have yet to provide proof of vaccination. That's roughly one third of the entire agency workforce.
"They are heroes of our workforce, but we need them to take one more, heroic step-which is to get vaccinated," MTA board member Neal Zuckerman said.
Transit workers are facing an ultimatum - get vaccinated by October 12 or submit to weekly testing. Some union leaders have predicted that large numbers of unvaccinated workers will sooner quit than comply. That, in an agency that is already struggling with a manpower shortage.
There are times when there aren't enough operators to run a full schedule of trains.
At the monthly board meeting, Lieber admitted that the percentage is low -- but that the number of vaccinated employees has increased 15% in the past five weeks.
He later told reporters that the vaccination rate is likely underreported.
"I think it would be seriously premature to start talking about doomsday scenarios where people are leaving their jobs," he said. "Our workforce has been heroic through COVID and they are trained professionals and highly valued. So nobody wants that. That scenario is unthinkable, and we don't think that's going to happen."
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