Which Pass to get

Hi,
You need to be more specific on how much time you will spend in each place. A 21 day pass would not work for the itinerary you give. A 14 day pass looks much better, but if you are OK with a 7 day pass going from Tokyo to Kansai and back, then a 7 day pass together with a JR East Nagano Niigata Area Pass might prove more useful and versatile for your 3 weeks overall.

Alternatively if you forego Nagoya, and are willing to see nearly all the other places within a week, you could get a Hokuriku Arch Pass and just buy regular tickets for between Nagano and Matsumoto. Yokohama is just a cheap ticket from Tokyo and not much concern.

You can see regular fares, routes and schedules on Hyperdia.
Under "More Options", be sure to uncheck the Nozomi box since you can't ride that train using the pass.

So again, there is no right answer here - you have to decide how much time you want to spend in each place, and then pick the best way to get there and back.

Good luck.