The highest mountain in Japan(till 1945 was Mt.Niitaka in Taiwan) and one of the famous and beautiful mountains on Earth. Mt.Fuji is not an extinct volcano but dormant one.
Mt. Fuji is located at the boundary of Yamanashi prefecture and Shizuoka prefecture. Therefore these two prefectures have big rivalry between each other regarding "where does Mt. Fuji belongs".
During nice weather, Mt. Fuji can be seen from the Tokaido shinkasen, approximately one hour after the departure from Tokyo station on the right hand side when the train is running through Shizuoka prefecture.
On the other hand, Mt. Fuji from Yamanashi prefecture is not a place to see from the train's window but the place to see much longer and slowly. There are 5 lakes beside Mt. Fuji. One of the 5 lakes and the biggest among them is lake Kawaguchi(Kawaguchi-ko)., which you can take lake cruise and enjoy the view of Mt.Fuji.
Kawaguchi-ko can be visited by Fuji-Kyuko line from JR Otsuki station on Chuo line. Take limited Express Kaiji from Shinjuku to Otsuki.