“There are a variety of problems with it. There are a variety of advantages. I will promise you this: that you and I and [Deputy Mayor Dan] Doctoroff will have a conversation about it,” Mr. Bloomberg said of the tunnel. “It’s not the world’s worst idea.”

In 2003, the Mayor included the tunnel in a list of transportation funding priorities given to local members of Congress. But at a March 2005 campaign stop in Middle Village, which is near the terminal where the trucks would be moved from rail cars onto the roads, Mr. Bloomberg reversed course, saying, “In this case, you really would destroy neighborhoods.”

In recent months, Bloomberg administration officials have defended the Mayor’s opposition by saying most of the trucks would have to go back to New Jersey anyway because that is where most of the region’s warehouse space is.