Where are Amazon employees going to live? Probably not out on Queens Boulevard on the 7/E/F/M/R so they'll be taking the train in the opposite direction. If they live on Long Island, they can take LIRR to Hunterspoint Ave (infrequent service, but demand can change that). If they live in New Jersey or in MNR territory, they'll take the train to Manhattan and then take the subway in the opposite direction from the main flow. If they live in Manhattan or Brooklyn, they're taking the train in the reverse peak direction; trains that are largely empty today because very few people do the reverse commute.

Similarly, JFK is 15 minutes to Jamaica on LIRR and 10 minutes on the Airtrain from there to the terminal. LGA... not super great. Probably take the 7/E/F/M/R to Jackson Heights/Roosevelt Ave. and transfer to the express bus (my preferred way of getting to LGA and I live in Brooklyn).

Finally, as I understand it they are going to use office space in the Citi tower... which is already built and I assume has had tenants throughout its life. So the transit problems were already understood.

All in all, I see this whole thing as completely non-newsworthy. 30,000 employees is nothing compared to the 1 million that already commute in to NYC from the suburbs and the 5 million that already take the subway.