The city's transit headaches, though, are far from over.
With some subway tunnels and stations still filled with water and power still off in downtown Manhattan, big gaps remain in the nation's largest public transit system even after the subways started rolling again Thursday morning.
New York Gov. Andrew Cuomo said there will be no subway service in Manhattan south of 34th Street, an area that includes the city's financial district and many tourist sites.
Commuters who would normally zoom beneath the East River in tunnels now flooded will have to disembark in Brooklyn or Queens and take shuttle buses across a handful of bridges, adding to the enormous stress already being placed on gridlocked Manhattan streets.
"We are going to need some patience and some tolerance," Cuomo said.
The Governor declared a Transportation Emergency on Wednesday night. That means that fares will be waived on commuter rails, buses and subways on Thursday and Friday in New York.
Below are the details for the plan to resume subway and related MTA services:
EFFECTIVE THURSDAY MORNING PRIOR TO RUSH HOUR
1 trains will operate local between 242nd Street (Bronx) and Times Square-42nd Street.
2 trains will operate between 241st Street (Bronx) and Times Square-42nd Street, with express service between 96th Street and Times Square.
3 trains are suspended.
4 trains will operate in two sections making all local stops:
5 trains will operate express in Brooklyn between Atlantic Avenue-Barclays Center and Flatbush Avenue.
6 trains will operate local between Pelham Bay Park and Grand Central-42nd Street.
7 trains are suspended.
42nd Street Shuttle S trains will operate between Times Square and Grand Central.
A trains will operate in two sections making all local stops:
B and C service is suspended.
D trains operate in two sections:
E trains are suspended.
F trains operate in two sections making all local stops:
G trains are suspended.
J trains operate between Jamaica Center and Hewes Street making all local stops.
L trains operate between Broadway Junction and rockaway Parkway making all local stops.
M trains operate between Myrtle Avenue-Broadway and Metropolitan Avenue.
N trains operate between Ditmars Blvd. (Queens) and 34th Street-Herald Square making all local stops.
Q trains are suspended.
R trains operate in Brooklyn between Jay Street-MetroTech and 95th Street making all local stops.
Both the Franklin Avenue and Rockaway Park S shuttles are suspended.
Click here for a map: http://www.mta.info/sites/default/files/pdf/HurricaneRecoveryMapOct312012.pdf
EFFECTIVE TOMORROW PRIOR TO RUSH HOUR
All shuttle buses will operate north on 3rd Avenue and south on Lexington Avenue.
1. Between Atlantic Avenue-Barclays Center and 57th Street-Lexington Avenue via the Manhattan Bridge
2. Between Jay Street-MetroTech and 57th Street-Lexington Avenue via the Manhattan Bridge
3. Between Hewes Street and 57th Street-Lexington Avenue via the Williamsburg Bridge
LONG ISLAND RAIL ROAD:
EFFECTIVE 2:00PM WEDNESDAY
Brooklyn - (Jamaica-Brooklyn): Hourly service
City Terminal ? (Jamaica - Penn Station): Resumed service
Ronkonkoma Branch: Hourly service from Ronkonkoma to Penn Station for AM rush hour Thursday, Nov. 1.
Port Washington Branch: Hourly service from Great Neck to Penn Station for AM rush hour Thursday, Nov. 1.
Babylon Branch: Suspended
Port Jefferson Branch: Suspended
Montauk Branch: Suspended
Hempstead Branch: Suspended
Long Beach: Suspended
Far Rockaway: Suspended
Oyster Bay Branch: Suspended
West Hempstead: Suspended
EFFECTIVE 2:00PM WEDNESDAY
Hudson Line: Suspended
Upper Harlem Line: Suspended
Lower Harlem Line: Restored with hourly service
New Haven Line: Suspended
New Canaan Branch: Suspended
Danbury Branch: Suspended
Waterbury Branch: Suspended
Pascack Valley: Suspended
Port Jervis: Suspended
BRIDGES AND TUNNELS
Robert F. Kennedy Bridge: Open
Henry Hudson Bridge: Open
Throgs Neck Bridge: Open
Bronx-Whitestone Bridge: Open
Verrazano-Narrows Bridge: Open
Marine Parkway-Gil Hodges Memorial Bridge: Open
Cross Bay Veterans Memorial: Open northbound to Broad Chanel; Open southbound to Rockaways but subject to period closures for emergency equipment
Hugh L. Carey Tunnel: Closed
Queens Midtown Tunnel: Closed
Get Eyewitness News Delivered