Long Island Rail Road
(Also "LIRR") The major main line rail provider on Long Island, part of the Metropolitan Transportation Authority of the state of New York. The railroad operates three main branches and several sub-branches serving the North Shore, South Shore, and central areas of the Island; the eastern terminus of all of these in New York City is Pennsylvania Station.
The LIRR was formed from a number of smaller local railways in the mid- and late 1800's, and rapidly became the primary commuter route for Long Islanders who had business in the City. It was acquired by the Pennsylvania Railroad in the early 1900's, and remained in Penn ownership until 1966, when it was acquired by New York State as one of the first parts of the new MTA.
Nita and Kit first use the LIRR in SYWTBAW, catching a train at its Freeport station when heading into Manhattan to get Nita's Fisher space pen out of Fred. There are various references to the LIRR scattered here and there through subsequent books, and it appears again (as a subway route originally part of the LIRR) in UL, where Kit and Nita take an alternate version of the rail road into another universe's Kennedy Spaceport.
(Recommended for further reading: LIRRHistory.com: aRRts aRRchives (informal history / gallery)