For mine I will go with the Erie terminal "based on", just considering how well it fit in such a confined space IRL.
My main aim, without seeming to be stuck up, will be to avoid doing yet another harlem station so mine will be in Brooklyn as the bush terminal has left an impression. Plus I'm a semi-modern modeler so the idea of New York as it appears in the movies from the 80's of a run down place, cold, wet, dark - very atmospheric, much like Prof Klyzrs (sp?) "New York 3A.M" micro that I absolutely love.
Plus there's conrail and every good layout needs conrail

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I think given my druthers I would incorporate an element of every line on a combined shelf/HCD arrangement that has bush terminal and their off street warehouses and 1st/39th junction, NY dock's Baltic st, Brooklyn Army and/or Naval terminal, the Rathole-esq arrangement that the EBDT used to go around the PRR N 4th terminal and probably throw in some El action, Long Island and a homage to the NYC highline in Manhattan.