Not sure how this eventually worked out for the OP, but I don't think that Amtrak stops at Princeton Junction. That is a NJ Transit stop only; Amtrak goes through w/o stopping. The OP could always board an Amtrak train at EWR (thereby earning the miles), and then transfer to NJ Transit at a common NJ Transit/Amtrak station. like MetroPark/New Brunswick/Newark Penn, buying the NJ Tranist ticket from the common station to Princeton Junction. That would probably also save a little $$, since for all trains that stop at EWR, there is a premium in those fares to offset the cost of the station