A friend of mine travelling to Japan soon has asked me the exact same question. It really depends. I think it depends a lot on whether this is the first visit to Japan, and on the weather. and even the day (i always found Hakone unbearably crowded during weekends). Most of the people I know were more impressed with Nikko on their first visit, but the temperature difference is bigger than I thought. Right now it is -2 degrees celsius in Nikko vs. 10 degrees in Hakone. So it might be best to decide on the spot, according to the weather that day.

It isn't.

I ended up deciding on Hakone. Since I'm visiting some shrines and the giant Buddha statue in Kamakura, as well as a visit to Kyoto, Nikko just seems like overkill with shrines for my trip. Hakone might be a nice change of pace with its hiking activities, Mount Fuji stuff, and Onsen.

A good choice, IMHO. Certainly no lack of hiking opportunities in Hakone.

I'd just get off at Hakone Yumoto station, walk past all of the storefronts, climb the first staircase into the mountain that you see while heading up the mountain, and go wherever the path takes you.

(BTW, plenty of mountain hiking opportunities in Kamakura as well!)

Are there organized hiking tours that you'd recommend? or should I just grab a hiking map at my hotel or something.

Just want to make sure you know the general consensus of the board regulars (me included)- Fuji is gorgeous from a distance, but often foggy and always barren up close. It is a volcanic mountain (brown, black and grey) and most think it isn't worth the climb. That said, I'm sure you can get find some really nice views in the Hakone area.

Yes, thats what I've heard. Fuji is better to look at, then to be in. Perhaps there's a good hike in Hakone that is geared towards giving some good Fuji views.