Like many routes in the US/Canada the NYC<->Montreal one is shared with freight, and for a significant distance on it there's only one track. Since the freight lines own the track they take priority, so the passenger trains have to go slowly, and often give way.

That route, picturesque though it is, is also not remotely economically viable. The parts of New York state it connects to are very poor compared to the endpoints, and it just doesn't get enough passengers. New York subsidise it to provide those communities with some links. (A drive through more remote parts of NY can be really depressing, but the Adirondacks are amazing).

The simple reality is an improved normal speed train service wouldn't make a difference, but the cost to build high speed is ridiculous either because the distances are too large or you're in already built up areas.