Hurricane Sandy left the best laid capital plans of New York-area transportation agencies in shambles, flooding tunnels, subway lines and LaGuardia Airport and rendering most area rail services inoperable.

Hardest hit is the Metropolitan Transportation Authority, which was already scratching for money before the superstorm dealt a massive blow to its subway system.

“I can say unequivocally that the MTA faced a disaster as devastating as it has ever faced,” MTA chairman Joseph Lhota said after the storm.

It’s too soon after the storm to say how much it will cost to repair damage to the MTA, or how much farebox revenue will be lost, let alone how it will all be paid for.

But it’s reasonable to assume that debt will help finance some of the physical recovery, said Alan Schankel, managing director at Janney Capital Markets in Philadelphia.

“There will be more borrowing for infrastructure. That’s a probability,” he said. “You’ll see a greater number of capital projects. These are tight times, and this will also lead to shifting priorities.”

Not only does it take time to tally the damage, but to learn how much outside support there will be for rebuilding.

Sen. Chuck Schumer, D-NY, at a press conference, said he plans to ask the federal government for 90% reimbursement on infrastructure. “The 90% is what’s called for and we are asking for that,” he said.

“We have yet to see what dollar amount help will come in in federal aid or state aid or how that will work, but these kinds of arrangements generally work out well,” Schankel said.

It will also take time to assess the true effect of the storm damage on the balance sheets of agencies and area governments.

“You could see some credit issues [such as downgrades] sporadically, but they will not be significant,” Schankel said.

New York Gov. Andrew Cuomo, speaking at a press conference, said Sandy should not be shrugged off as a once-in-a-lifetime event.

“It’s short-sighted for us to say that this is a once-in-a-generation happening,” he said.

We have to reconstruct in a way that modernizes and reforms our infrastructure. We’re not built in a way that has built-in protections,” Cuomo said. “It’s for a longer conversation, but part of the learning is that climate change is a reality.”

In the meantime, work was underway to restore services.

New York City buses began running limited service Tuesday afternoon.

Wednesday, Cuomo announced that as of Wednesday afternoon, the Long Island Rail Road and Metro-North Railroad, both part of MTA, will begin to provide limited service. New Jersey Transit commuter trains remained suspended until further notice.

He also announced that beginning Thursday morning, there will be limited subway service on several routes, supplemented by a bus shuttle between Downtown Brooklyn and Midtown.

Transportation agencies were far from the only ones impacted by the storm.

Reports were still trickling in Wednesday from New Jersey, where the Jersey Shore took the full brunt of the hurricane’s force.

“I never thought I’d see what I saw today. Ever,” Gov. Chris Christie said late Tuesday after inspecting the damage.

Long Island was also hit hard by the storm.

On the island’s south shore, the city of Long Beach, already facing a financial crisis, was pummeled by the storm, which left the city without functioning water or sewer systems.

“We have no estimates yet. Estimates regarding restoration or cost is anybody’s guess,” said City Manager Jack Schnirman.

The public Long Island Power Authority took the brunt of the storm. LIPA serves roughly 1.1 million customers in Nassau County, Suffolk County, and a portion of Queens County.

The vast majority of them were without power in the storm’s aftermath.

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