I agree about checking our Bernard's work.
Here is a google map
of some of the places I managed visit when I lived in Japan.
When you click on a pin, it will open a window with a images (unless the pin is red, they don't have images).
There is also a link to my old flickr page that has images in sets by their location. This could help find some places?
You can also check out my website
In terms of pure landscape locations you may have to travel a fair bit to get out of the cities.
If you will be driving to Mt Fuji from Kyoto, you may want to consider diverting via Kamikochi
, it will be a fair side trip but depending on the time of year, could be well worth it.
Mt Fuji is renowned for not being visible due to cloud and there is a high chance you wont be able to see it.
If you had more time, I would suggest Yakushima. It is stunningly beautiful, but quite remote from where you fly in/out.Japan-Guide
is a very useful website.
Enjoy your trip