The estimates in the first link you provided pegs travel time at 6 hours from NYC to Niagara Falls. Albany is already less than 3 hours on the Amtrak from NYC, but is still failing to "shed development pressure" from NYC. It's a chicken-and-egg problem: how do you convince jobs to move upstate without people, and how do you convince people to move upstate without jobs? Adding a train isn't enough unless it's quick enough to be a daily commute. There are other ways to entice residents but, at least in Albany's case, restrictive zoning and land use laws get in the way.
In the 1950s, the US federal government decided to go all-in on highways for medium and long distance travel. It would be costly to attempt to switch back to long distance rail now and would have a deep impact on American life. The reasons rail is so desirable in an urban context doesn't often translate to a medium or long distance route.
> even the most expensive improvements under consideration at $15 billion are cheaper than projects in NYC such as the Second Avenue subway (estimated completion at $17 billion for 8.5 miles!)
Sure, but in terms of how many people would be served by the 2nd Ave subway vs a long distance cross-state route (200k/day on the 2nd Ave subway vs 4m/year on the train line), it seems less absurd to invest that magnitude of funding on the subway.