Another place that I visited during my vacation in Japan was Hakone. It is a mountainous town in Kanagawa Prefecture. To reach the town, you can take JR Train from Tokyo Station to Odawara Station for 30-40 minutes and then change to bus. The bus can be found just outside the station. I recommend you to buy a Hakone Free Pass during the trip as it can be used for buses, trains, cable-cars, ropeways and sightseeing boats. The price is reasonable. The 2 day pass will cost you 3900 yen if you buy it from Odawara Station.
Hakone is renowned for its hot spring resort/onsen and ryokan. There are a lot of onsen opened there from the traditional to modern ones. One of the famous hot spring in the area is Kowadukani Yunessun. The location can be easily accessed by public transportation yet the admission fee is quite expensive compare to the other resorts.