Monday, the MTA said service resumed at 5 a.m.
"With very limited exceptions, service has resumed across the subway system on all lines, including service to and from Far Rockaway," the agency said in a statement on its website. "However, service will be less frequent than normal, and customers should expect longer waits and more crowded trains. Frequency of service will improve over the course of the day."
The New York City subway system is the largest public transportation system in the U.S., both in terms of miles and the number of passengers. The system carries 1.6 billion passengers a year.
Officials in Philadelphia also shut down public transportation there, closing the Southeastern Pennsylvania Transportation Authority Sunday morning shortly after midnight.
SEPTA, the sixth busiest public transportation system in the country, said Monday that some trains and buses were operating on a normal schedule Monday, while others "will operate with detours, delays, and possible disruptions due to flooding conditions, and street obstructions."
Washington, D.C.'s Metrorail, the nation's second busiest subway system, never stopped operating during Irene, though officials said ridership dropped 67 percent Saturday from the weekend before amid warnings about Irene. The Washington Area Metropolitan Transit Authority said Metro had 128,390 riders Saturday, compared to 345,425 on Aug. 20.
The system said bus costumers "should expect possible detours around downed wires and trees and allow additional travel time."
The national passenger rail service, Amtrak, said Monday that most of its regional service between Washington and Philadelphia had resumed, but trains were still canceled between Philadelphia and Boston.