Reddit reviews Lonely Planet Hiking in Japan (Travel Guide)
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Hey there, I think I may be able to help you!
I spent a month in Japan hiking and hitch-hiking, as well as over 6 months living/working there. Mt.Fuji was very high on my to-do list, but I'd missed the season and was strongly advised against doing it, despite having a fair level of experience and being just about a month too late. The official season is from July 1st - August 31st. It's fairly obvious why you can't go in winter, and the main reason for being unable to go in Autumn and Spring would be unreliable/bad weather and the facilities closing down. People do go outside of the season of course, and one of the best times may be two weeks either end of the season - you won't be fighting the crowds, conditions should be alright.
As for going in May, I would advise against it and wouldn't do it myself despite having done plenty of hiking elsewhere. As far as I know, nothing is physically stopping you going whenever you want, so it will never be closed as such. Some enthusiasts (and professionals) will go up mid-winter.
I'll answer the rest of your questions anyway though, and then give you a few pointers/other ideas.
Getting There/Base
Getting a train or bus from Tokyo is easy, there are plenty of them (a lot more during the season though). A bus would be cheaper. I don't think you'll be able to get public transport to the 5th base (where most people hike from to the top) easily off season, so it might require taking a return taxi from Fujiyoshida. If you want more specifics, I can look into this quite easily. If you're not travelling onwards and further south, or planning on staying in the area, it's very easy just to use Tokyo as a base. I'm pretty sure this is the thing most people do - just make it an overnight trip from Tokyo.
Sunrise/Sunset
Sunrise is the one people go to Mt.Fuji to see, and in season most of the transport from Tokyo is geared up for this - they'll take you to the right place to walk up in time for the sunrise, then you can hike back down and get back.
Alternatives
Like I said, I don't think going in May is the best of ideas unless you have a good level of experience under your belt. If you decide to go ahead with it, make sure you leave your information with the police in Yoshida.
A great alternative would be doing a hike in the Fuji 5 Lakes area. This is at the base of Mt.Fuji, so you'll have amazing views of the mountain and the surrounding area. I haven't hiked there myself, but I can find more info if this sounds interesting to you. You can do this as a day trip from Tokyo, or spend a little longer if you have the time.
From your post it sounds like you're looking for a 2 day trip from Tokyo with hiking involved. A place I can't recommend enough would be Nikko National Park a few hours by train to the north of Tokyo. You'll be spoiled for choices of things to do here and I would go again at the drop of a hat. There are some amazing hikes around the area and plenty of shrines and historical sites to see as well if that's your thing. One hike near there which I did takes you through a stunning marsh with all kinds of flora and leads to the hot spring town of Yumoto Onsen, a great place to soak your bones after a long day's walk. Again, if you'd like more info about these places just ask and I'll flesh it out a bit more.
Further Info
I don't know too much about it but there is lots of hiking in most areas of Japan. If you can find it check out Lonely Plant's Hiking in Japan book or something similar. There isn't too much detailed information on hiking in Japan in English that I know of. Maybe someone might know of a good info site.
This book should help