We stayed three nights in the Akarinoyado area of Nikko (property listing, $140 per night including tax and breakfast). Our three nights visiting the forest temples of Nikko was an easy shinkansen train ride from the Tokyo area. Accommodations were simple, comfortable and affordable. Without a car, prepare to walk, taxi or bus. It is a pleasant 25 minute walk from here to the Nikko train station. Very well run family inn. Breakfast was a work of art! Onsen included in price.
OUR HOTEL STAYS IN JAPAN
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Righa Royal Kyoto - Kyoto Prefecture
Merveille Hakone Gora - Hakone, Kanagawa Prefecture
Hotel Okura Tokyo - Tokyo Prefecture
Hotel Mystay Fuji Onsen Resort - Fujiyoshida,Yamanashi Prefecture
Montein Hotel - Kitakami, Iwate Prefecture
Nikko Akarinoyado Villa Revage - Nikko, Tochigi Prefecture