That's ridiculous. Excluding the subway, there's still approximately 110k riders each way on the LIRR[1] and 90k each way on NJ Transit[2]. Plus amtrak, you're talking about ~450,000 daily rail passengers. That would still make Penn Station one of the 3 busiest train stations in Europe, for context.

[1] http://transitdocs.com/files/data/lirr/2012RidershipBook.pdf [2] http://www.njtransit.com/pdf/FactsAtaGlance.pdf