The transit infrastructure argument is moot. Here's transit reporter Aaron Gordon making the case far better than I could:
> The G, 7, E, M, F, R, N, and W are all within a reasonable walking distance from the proposed HQ site. In the short term, Amazon will occupy one million square feet of 1 Court Square, which sits directly above…Court Square on the E, M, 7, and G lines (the other aforementioned lines are not far away). While they’re all crowded during rush hour and Court Square itself will strain under the ridership (but less so than during the L shutdown) the G and M have additional peak-direction capacity. Also, they’re all well below the current crowding levels on the L and 4/5.
Further, there’s good reason to believe many Amazon workers will follow non-traditional commuting patterns. For starters, a number of them will probably live within walking or bicycling distance from HQ2 given the housing construction boom in the neighborhood. For those who don’t, many will reverse-commute from Manhattan (Hudson Yards, the other NYC neighborhood experiencing a housing construction boom, is straight down the 7). For workers looking to commute from the suburbs, LIC has two LIRR stops, although they currently don’t have very attractive service patterns. Some might even choose to live in Metro North country, given that LIC is one stop on the 7 from Grand Central. It’s also worth noting that East Side Access service, which would bring the LIRR to Grand Central, is slated to begin in December 2022, making Long Island a more attractive option.
The point is not that any one of these options will be most attractive to future Amazon employees, but all of them will attract some and the load will be dispersed. This is the beauty of a robust, healthy transit network: it can absorb even the biggest of shocks.
40000 people across 8 lines with a bunch of countercyclical commuters is a drop in the bucket in NY transit.