I’d investigate Hakone first as volcanic activity has been closing off areas in recent months/years. In ideal conditions it involves less walking than Nikko as lots of ground is covered by ropeways, cable cars and boats (using Hakone Free pass). This might suit you better.

Jigokudani near Nagoya was fascinating to me as an about to be mother, I learned my most useful lessons for parenting from the macaques there and spent hours observing and pondering behaviour. It’s only now that my kid is much older that I’m starting to consider going back. Not a destination I’d suggest for a young child. To get the most out of this place (IMHO) some basic understanding of underlying behaviour and lots of patience are required.
Doesn’t surprise me when I see people write about being a bit bored there.

I gave you quite a few suggestions but still see no feedback so have nothing further to add.