Metro-North's Hudson Line, the last of the commuter rail's three major routes to return,  began limited service Friday between Grand Central and Croton-Harmon. 

The Hudson line had posed the most significant challenges for Metro-North workers, Metropolitan Transportation Authority officials said.

Trees that had fallen on tracks had to be removed. Signals at several stations were so badly damaged by water that they need to be replaced. And rail cars stocked with ballast had to be brought in to repair washout-damaged structures that support rail lines between Croton-Harmon and Carlstadt.

"It's a very challenging operation," Metro-North spokeswoman Marjorie Anders said.

The opening of the Hudson Line should make things easier for commuters like James Kaplan, a writer from Hastings.

On Thursday, he was going to a party in New York City but had to head over to the Harlem Line station in Scarsdale, adding 90 minutes to his usual 30-minute ride into the city.

advertisement | advertise on newsday

"I missed a train because I went down several roads with trees across them, and had to double back," Kaplan said.

Meanwhile, Metro-North's Harlem Line inched closer to full service  with the opening of the Southeast station in Brewster.

The first of a limited number of inbound and outbound trains left Southeast Thursday for Grand Central Station at 2:13 p.m. By Friday morning's rush, full service was restored between the two stations.

The last leg of the Harlem Line yet to open is the Wassaic branch, which carries some 900 customers on a typical weekday. Nearby substations at Katonah and Bedford Hills, which power the branch, were damaged by flooding after Hurricane Sandy touched down Monday night. Metro-North is working with NYSEG to restore power.

Along the New Haven Line, some 135 trains streamed between Stamford, Conn., and Grand Central on Thursday. Power outages remain at stations as far north as New Haven. Connecticut Light and Power is at work trying to restore power to those stations.

More commuting good news was unveiled Thursday night, as Gov. Andrew Cuomo announced that additional service was restored on the New York City subways with the M line up and running in Queens in time for the evening rush and limited 7 trains to be offered in Queens between Main Street and 74th-Broadway before the night was over. With the M and 7 trains in operation, 15 of the city 23 subway lines have reopened in some fashion.

There still is no subway service below 34th Street in Manhattan while the MTA tries to clear tunnels flooded by water. Commuters were directed to downtown buses they could pick up at Second, Fifth or Lexington avenues.

"As we have said from the beginning, we will bring service back on a gradual basis as we are able to do so. The subway system will be a shifting landscape for some time to come," MTA Chairman Joseph Lhota said. "But we are making steady progress toward some level of normalcy."

advertisement | advertise on newsday

Cuomo waived fares on subways and rail lines through midnight Friday in an effort to get people out of cars on Manhattan's traffic-choked streets and into public transportation. A three-person minimum is in effect for cars traveling on the East River bridges, the Lincoln Tunnel and the RFK and Henry Hudson bridges from 6 a.m. to midnight Thursday and Friday.

Meanwhile, one tube of the Holland Tunnel reopened to buses Friday morning. Additionally, all of New York region's major airports have been reopened.

Lhota did get some good news from the federal government Thursday. The Federal Emergency Management Agency has agreed to pick up the tab for transportation-related costs the agency has incurred from the time Sandy hit through Nov. 9.

Lhota estimated the nation's largest transit system is losing $18 million per day in revenue. It's money the cash-crunched agency can ill afford to lose. The MTA is trying to close a $450 million hole in next year's $12.6 billion budget.