Where to go during Autumn Colors season?

I am planning to go to Japan in November and think as to where to stay for first 5 days to enjoy Autumn colors. I would like a traditional ryokan, preferably with onsens. But most importantly I would like to have a great view from there or/and be able to go for a walk/hike into mountains or something, again to enjoy the beauty of nature.

I am currently looking into Hakone, Nikko, Kyoto, Nagoya, Kurobe regions. But they are popular and quite booked up already. I am sure there are many more places in less known areas, so would like to get some suggestions.

This page lists some of the best autumn color destinations with their usual best timing of the colors:
http://www.japan-guide.com/e/e2014_when.html

I am currently looking into Hakone, Nikko, Kyoto, Nagoya, Kurobe regions

I have yet to see good autumn colors in Hakone (despite multiple autumn trips there). The colors in Nikko tend to be best in October, so I think you are a little late. Kyoto has some of the best colors in all of Japan, but it is not strong with respect to hiking and onsen. And it is foremost a city where nature is rather limited. Korankei is a very nice but crowded spot near Nagoya. I don't think it has onsen or traditional ryokan, and the hiking trail network is rather small. The Kurobe Gorge could be a suitable destination, though:
http://www.japan-guide.com/e/e7575.html