The ideas on improving travel across the Hudson are part of the latest update to the association’s sweeping regional plan, the fourth edition of which is scheduled to be released this fall. The association is a nonpartisan research group that has helped to shape transportation in the New York metropolitan region for decades. Its suggestions are not entirely new. The planners of the Gateway project have considered expanding Penn Station to the south and extending the tunnels across Manhattan and have not ruled out either idea.

Thomas K. Wright, the president of the association, said it did not have detailed estimates of the costs of these projects. But he said the extension of the Gateway tunnels across Manhattan and under the East River to Queens could cost about $7 billion. That would push the total cost of Gateway, half of which is expected to be provided by the federal government, well past $35 billion.

Alluding to the Trump administration, Mr. Wright said the planners of Gateway had been “having trouble getting the money that we need from the feds already”

Still, he said, he believed that the recommendations would be cost-effective solutions to dealing with the overcrowding on trains on buses. Running trains through Manhattan between Long Island and New Jersey would increase the potential capacity on trains crossing the Hudson by about 40 percent, he said. Under this proposal, those trains that are now operated by the Long Island Rail Road and New Jersey Transit, would essentially combine territories, picking up passengers both east and west of Manhattan. (Neither the Long Island Rail Road nor New Jersey Transit has suggested such a proposal.)

Mr. Wright said he did not know how much a bus terminal in the basement of the Javits Center would cost. But he said building it would allow the Port Authority to save billions of dollars by rehabilitating rather than replacing the main bus terminal in the next 25 years.