For whatever it's worth Congresswoman Maloney is pushing for the stop that was promised in the early stages of the ESA project.
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She's not wrong: The powers that be have in the past talked up building a big transit/rail hub there which would also connect all the subway routes (the 7, N & W don't connect to the E, F, M, R downstairs).
None of this will happen of course. If I recall right the ESA plan was just two platforms in the middle of Harold. This scenario seems to be what Maloney is pushing for. Amtrak could stop at those same platforms if they wanted... (yes, I know, it'll kill the schedule etc).
As for Amazon, they need the tech talent in NYC - NYC, and certainly not LIC, doesn't need them. LIC has obviously grown (faster that anywhere else in this country) and will keep growing with or without Amazon. The overall sentiment is if they want to come here they can pay their fair share of taxes like the rest of us... so you know, maybe we can afford to reopen the firehouses Bloomberg closed and maybe fix our decaying infrastructure.
Plenty of other cities could use a boost from having Amazon go wherever. LIC, and NYC on a whole, will keep growing with or without them. I'll be surprised if there isn't an NEC stop here within the next 20-30 years, if not much sooner.