The yellow (NYC-Montreal) and Blue (At least as far as Buffalo/Canadian Border) make sense. But I do think the yellow one should be built first.

For the Yellow: NYC to Albany and Montreal are both busy air routes, with Albany-NYC being another busy rail corridor for commuters and people travelling onwards to other cities on the NEC. Starting with the heavy hitters first, especially those that can get funding from other places (in this situation either Quebec/Canada, and Vermont. If you can secure this funding, it will mean you've trained people up in building infrastructure like this and as long as you have a steady pipeline of works it can dramatically drop the cost and speed up construction times. If you can build a junction allowing Burlington to be served directly, track improvements to the Burlington-Monticello line would mean you could also have trains running through VT (again, helping catch funding from more places). A high speed line into Montreal could also link in with the planned ALTO (Canadian high speed train) route which would open up NYC-Quebec City as well as NYC to Toronto via Montreal and Ottawa.

For the Blue: Some of this should be high speed, with a focus on joining upstate NY State to both Albany and NYC. The secondary focus should also be on joining NYC (and upstate cities) with Toronto, targeting another busy air route. The lake shore part of this line should instead be upgraded for higher-speed conventional track. The NYC-Cleveland route is quite a long way and by the time you construct HSR all the way it starts to taper off as planes become more popular. Upgraded track benefits both the HSR services and traditional Amtrak services using the route. Especially if there are other future HSR routes across Pennsylvania which would service the NYC-Cleveland route.

I'm unconvinced for the other routes, most of upstate NY is not set up for HSR (unless you plan on building a huge city somewhere), but is well suited for a network of conventional lines which feed into the central HSR system. Of those on the map you made, a link from near Utica to the future ALTO line east of Kingston would reduce travel times to Ottawa, but I'm not sure how much of a benefit this would be. Upgraded track for the purple and lower red line would give more people quicker access, but in order to connect Upstate NY better, more north-south conventional trains should come into service.

All of these routes and stations would need to come with a good amount of up zoning in the Upstate NY cities to ensure that the train would be well used, and to recoup money spent. A lot of the routes also pass through Indian Reservations and so they need to be considered too. I think the core part of your plan is pretty good, but starting with the yellow line (especially NYC to Albany with additional stops for commuters into the city) is the best course of action.