Take a Kodama or Hikari train along the JR Tokaido Shinkansen from Tokyo to Mishima Station. Then, take the JR Tokaido Line from Mishima to Fuji Station and transfer to the JR Minobu Line to Fujinomiya. The entire journey takes around two hours and costs about 4500 yen. The trip is fully covered by the Japan Rail Pass.
Alternatively, take a local train on the JR Tokaido Line from Tokyo to Fuji Station (requires a transfer at Atami) and change to the JR Minobu Line to Fujinomiya. The trip takes about three hours and costs 2640 yen. There are 2-3 connections per hour.
By train and bus
2 h
¥5,500
Take a Kodama train along the JR Tokaido Shinkansen from Tokyo to Shin-Fuji Station (70 minutes, about 5000 yen one way, two departures per hour). From Shin-Fuji Station, there are 3-4 buses per day bound for the Fuji Five Lakes, which stop at Fujinomiya Station (35 minutes, 570 yen) and the Shiraito Falls (1 hour, 1080 yen) along the way. The shinkansen is fully covered by the Japan Rail Pass, but the bus is not.
By bus
2.5 h
¥2,750
JR Kanto Bus and Fujikyu Bus operate highway buses every 2-3 hours (more during rush hours) between Tokyo Station (Yaesu South Exit) and Fujinomiya Station. The one way trip takes about 2.5 hours and cost 2750 yen. There are 9-10 departures per day in each direction. One bus per day continues on past Fujinomiya Station to the Shiraito Falls (three hours, 3400 yen).
Above fees and schedules are subject to change. Be sure to check current yen exchange rates.
Another transportation hub is Shin-Fuji Station along the Tokaido Shinkansen, which is served only by Kodama trains. From Shin-Fuji Station, there are infrequent buses to Fujinomiya Station, Shiraito Falls and the Fuji Five Lakes. Note that local trains stop at Fuji Station, which is 1.5 kilometers away and not served by many of the buses in direction of the Fuji Five Lakes.
The Mount Fuji West Side Story Passport provides two days of unlimited use of buses on the west and north side of Mount Fuji for 2500 yen, including the bus between Shin-Fuji Station and Kawaguchiko Station and the tourist buses around Lake Kawaguchiko and Lake Saiko. In addition it provides discounts at selected tourist attractions, shops and restaurants. The pass can be purchased at Shin-Fuji, Fujinomiya, Kawaguchiko and Fujisan stations.
Despite all the buses that run though the area, the connections around Fujinomiya may not be very convenient for those wishing to visit multiple sites in a day. Those visitors may be better off exploring the area by rental car. Rental car outlets can be found around Shin-Fuji and Kawaguchiko Stations.