A subsidiary of the Anacostia Rail Holdings Company, NY&A operates exclusively on Long Island and is connected to the U.S. mainland via CSX's Fremont Secondary over the Hell Gate Bridge.

[1] Lumber, building products, scrap metal, construction & demolition debris, bio-diesel fuel, food, beer, gravel, propane, chemicals, structural steel, plastics and recyclable cardboard/paper are the NYA's main traffic.

[4] Team tracks are located in Bay Ridge, Hicksville, Huntington, Greenlawn, St. James, Islip, Richmond Hill, Maspeth, Speonk, Medford, Southold, and elsewhere on the Long Island Rail Road (LIRR) lines that NYA serves.

[5] In 2014, work was underway to build a transload facility for vegetable oil, food products and construction material at NYA's Wheel Spur Yard along Newtown Creek near Long Island City.

[1] About 15 percent of freight cars transported by the NYA are floated across New York Harbor from Jersey City to NYNJ Rails's railyard in Bay Ridge on the Brooklyn waterfront.

[3] July 8, 2015 – An NYA freight train smashed into a tractor trailer after the crossing gates went down slowly in Maspeth, Queens; the truck driver escaped with minor injuries.

June 17, 2021 – NYA Train RS41, consisting of Locomotives 300 and 271, was rear ended by Long Island Rail Road Inspection Car TC82 east of the Cold Spring Harbor station.