A number of proposals have been put forward to increase the share of rail freight movement within the City and Long Island:

• Construction of an intermodal rail-to-truck yard at a 100 acres (0.40 km2) site in the West Maspeth section of Queens. The location is near the intersection of Interstate 278 and Interstate 495. The project has received intense opposition for neighbors concerned about increased truck traffic on local streets that lead to the highway interchange. A City University of New York (CUNY) study pointed out that "no current demand for a containerized truck-rail facility has yet been demonstrated" in part because intermodal containers generally must be unloaded at major distribution centers, few of which are located on Long Island.[2](p22) The study also noted that standard double stack rail equipment is too wide to run on tracks where third rail is used, as it is on much of the Long Island Railroad's passenger routes.
• Construction of a transload facility at the former Pilgrim State Hospital. This project has also been stymied by local opposition, though Governor Paterson vetoed a 2008 bill that would have killed the project by incorporating the site into a nearby state park. The same CUNY study, commissioned by the state after the veto, concluded that "there is an immediate demand for bulk service"—rail-shipped commodities such as building materials, plastics, paper, and food—that was unmet due to a lack of transloading facilities on Long Island. It identified 12 additional candidate sites besides Pilgrim State, including the Brookhaven Rail Terminal that has since opened.[2](p3, 5, 8, 16)
• Rebuilding parts of the Hunts Point Cooperative Market in the Bronx, already a major rail freight destination, to facilitate greater rail use. The market received a $10 million grant in 2012 for this purpose.[24]
• Construction of a double-stack-ready Cross Harbor Rail Tunnel from Greenville, New Jersey to Brooklyn, at a cost estimated in 2004 at between $4.8 and $7.4 billion, depending on whether one or two tracks are provided.[25] The Port Authority is preparing a new environmental impact statement for the project,[25] which has come under criticism because of its high cost (all the US freight railroads combined spent $10.7 billion on capital expenditures in 2010[26]), modest projected impact on overall truck traffic (around a 5% reduction) and potential impact on local communities, such as West Maspeth.
• Building a new container port on Brooklyn’s Sunset Park waterfront with a rail link to the proposed tunnel. Brooklyn currently has a container operation at Red Hook, but it has no rail connection. (Sea access to Brooklyn is not obstructed by the Bayonne Bridge.)