The New York Connecting Railroad was built in 1916-17 as a joint venture between the Pennsylvania Railroad and the New York, New Haven & Hartford. The line's northern endpoint is at Port Morris, in the south Bronx. There is no physical connection; the tracks simply continue northward as the former New Haven mainline.

Just south of Port Morris is the line's most significant structure, the 1,000-foot Hell Gate Bridge, which crosses the East River at a point known as Hell's Gate for its unusually turbulent water.

The NYCRR continues on a concrete viaduct which rises high above Astoria. The elevated Ditmars Boulevard station on the N Train is partially located within one of the arches. The line begins to curve southward again and parallels the Brooklyn Queens Expressway before splitting up into a freight and a passenger line near 30th Avenue in Woodside.

The passenger line curves back to the west and winds up in the Long Island Rail Road's Sunnyside Yards. This was originally used by New Haven passenger trains departing from Penn Station, and is now used by Amtrak.

The freight line continues south, roughly following 69th Street in an open cut to Glendale, where it interchanges with two former LIRR freight lines, the east-west "Montauk" and the Bay Ridge Branch, which continues in a southwesterly direction to the Brooklyn waterfront.

Prior to the NYCRR's construction, Pennsylvania Railroad freight bound for New England was ferried for 14 miles between New Jersey and the south Bronx, across the Hudson and East Rivers. The NYCRR saved several hours' travel time, as well as loading and unloading time.

The NYCRR was folded into Penn Central in 1968 along with both of its parent railroads, and ownership then passed to Amtrak in the early 1970s, becoming part of its key Northeast Corridor line between Boston and Washington. Freight operations had been provided by Conrail and are now provided by CSX.

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