In the fall of 1961, the plans for the Trade Center shifted to the west side, on the Hudson River waterfront. New Jersey officials had resisted approving a Port Authority project that was unconnected with their state's development and transit needs. Delays followed, and a Port Authority planner then suggested the center be shifted to the west side, where it could be linked to the bankrupt Hudson and Manhattan Railroad, which carried commuters from Newark and Hudson County. In the spring of 1962, the two states approved the new location, and the Trade Center legislation was joined with the Port agency's purchase and modernization of the rail line (now PATH).

The new site included the Hudson and Manhattan Terminal, a pair of 22-story office buildings on Church Street between Cortland and Fulton, which on completion in 1909 constituted - like the later Twin Towers - the largest office complex in the world.

Another important part of the political solution to the west side site was the agreement with New York City to use the excavated dirt of the Trade Center foundations as landfill for the first 23 acres of Battery Park City.