Yaphank is on the Greenport Branch, it only has limited passenger service but there is a freight siding for Georgia-Pacific right by the station.
During the 1930's many German families sent their kids to Bund (brotherhood) pro-Nazi camps in Yaphank on the weekends. This was in response to Hitler's call for all overseas Germans to return to the Fatherland, those who didn't tried to be pro-Nazi in other ways like these camps. In fact, there is a song called, "Yaphank Used To Be A Nazi Town" but I don't remember who sings it.
But if you want to read about Nazis and the LIRR you should investigate the sabotage mission of 1942. Four Nazi spies landed in Montauk and took the LIRR to Penn Station on their way to sabotage a factory in Pennsylvania. There were not sucessful and were caught in Manhattan.
http://www.montauklife.com/history_nigh ... nazis.html