Gov. Dannel P. Malloy and the Metropolitan Transportation Authority had some good news for Stamford-New York commuters on Wednesday: Metro-North will resume service between Stamford and Manhattan on the New Haven Line starting Thursday at 4:43 a.m. About half of New Haven line commuters shuttle between the cities on a daily basis.

Service will be free for Thursday and Friday.

The restoration of service has come more quickly than many expected, given the tremendous number of trees down on the New Haven line and destruction of catenary wires — overhead lines that transmit electrical energy to the trains. The wires were already in need of extensive repair before the storm hit.

But Metro-North still doesn’t know when service might be restored for stations north of Stamford, or for the New Canaan, Danbury and Waterbury branch lines.

“We have not had time to focus on [the branch lines] yet,” Metro-North spokeswoman Marjorie Anders said Wednesday afternoon. The Waterbury and Danbury branches are in “pretty good shape,” she said, but the New Canaan branch line took a much harder hit.

“We took one look at New Canaan and said we can’t do this first,’ ” Anders said. Metro-North might look into providing temporary bus service for those commuters. Both Anders and Malloy said they expect at least limited service on all of New Haven’s main line to be restored before the weekend.

For Connecticut commuters coming from anywhere north of Stamford, options for getting into New York City are few and far between. Greyhound service into and out of Manhattan is still suspended, though it will operate on a limited basis starting midday Thursday.

“There’s flooding, there’s power lines that are down throughout the area,” Greyhound spokesman Tim Stokes said. “Passengers are having trouble getting to our location [at the Port Authority], and so are employees.”

Nor is driving a good option. New York City Mayor Michael Bloomberg announced on Wednesday that cars with fewer than three passengers will not be allowed to enter Manhattan through most major bridges and tunnels because of congestion already on the streets.

And of course, once commuters get to New York, things may not get any easier. MTA Chairman Joe Lhota has called Hurricane Sandy the “worst disaster” to hit the New York subway system in its 108-year history. But limited service on the subway system will resume Thursday morning, including key routes for Metro-North riders, such as the shuttle from Grand Central Station to Times Square and the “4” line between Woodlawn and Grand Central.

Despite significant damage to the New Haven line, Anders echoed a line spoken by many across Connecticut in the past few days — it could have been much worse. The New Haven rail yard, which is prone to significant flooding even in much smaller storms, was spared. That means key equipment and rail cars are safe.

For some advice on creative ways to get from New Haven to New York tomorrow, visit our commuter blog, Rant & Rail.