Depending on whether you plan on visiting the southern region or the northern region of the Shin-etsu Trail, there are two train routes coming up from Tokyo. Transportation from the train station to lodgings is provided. Transportation from lodgings to the Shin-etsu Trail may be arranged upon request.

Taking the JR Hokuriku Shinkansen to the JR Iiyama Line:

This route is recommended for those who want to visit the southern and central areas of the Shin-etsu Trail.

From Tokyo Station, take the Hokuriku Shinkansen to Iiyama Station. It usually takes about 30 minutes from Iiyama Station to Mt.Madarao Trail Head by bus. Depending on which area you plan on visiting, you can take the JR Iiyama Line and get off at Togarinozawa-Onsen Station, Morimiyanohara Station as well as other stations further down the line.

Taking the Jōetsu Shinkansen to the Hokuetsu Express Hokuhoku Line

This route is recommended if you plan on visiting mainly the northern area of the Shin-etsu Trail.

From Tokyo Station, take the Jōetsu Shinkansen to Echigo Yuzawa Station and transfer to the Hokuetsu Express Hokuhoku Line. Depending on where you wish to go, you may want to transfer to the JR Iiyama Line at Tōkamachi Station

HyperDia is a service which offers the route and the timetable of the railway and the aviation of Japan.
http://www.hyperdia.com/en/
Please fill the blank "from Narita, Haneda or Niigata Airport" and "to Iiyama, Morimiyanohara or Matsudai Station".

If traveling by car, there are two routes coming up from Tokyo. One leads to the northern region of the Shin-etsu Trail, and the other leads to the southern region. Choose your route based on which section you plan on going to.

Access via the Kan-etsu Expressway and Jōshin-etsu Expressway

Use this route if you plan on visiting the southern region of the Shin-etsu Trail.

Coming in from the Kan-etsu Expressway, get onto the Jōshin-etsu Expressway at the Fujioka Junction (JCT). Next, take the Kōshoku JCT toward Nagano and Shin-etsu. Exit off the expressway at the Toyota-Iiyama Interchange (IC) (233 km past the Nerima IC, about 2 hours and 40 minutes). Following ordinary roads from here, it takes between 20 and 60 minutes to get to respective areas of the Shin-etsu Trail.

Access via the Kan-etsu Expressway only

Use this route if you plan on visiting the northern region of the Shin-etsu Trail. Exit at the Shiozawa-Ishiuchi IC (176km past the Nerima IC, about 2 hours) and continue on ordinary roads through Tsunan. It takes between 50 and 70 minutes to reach respective areas of the northern region of the Shin-etsu Trail from here.

Coming from Matsumoto Airport (Nagano Prefecture)

Take the Shiojiri Kita IC to get onto the Nagano Expressway. Next, get onto the Jōshin-etsu Expressway at the Kōshoku Junction toward Nagano and Shin-etsu. Exit off the expressway at the Toyota-Iiyama IC (93km past the Shiojiri Kita IC, about 1 hour). Using ordinary roads from here, it takes between 20 and 60 minutes to get to respective areas of the Shin-etsu Trail.

Coming in from Niigata Airport (Niigata Prefecture)

Take the Niigata Airport IC to get onto the Hokuriku Expressway, heading southwest. To get to the central and northern zones of the Shin-etsu Trail, take either the Kakizaki IC (112km past the Niigata Airport IC, about 1 hour and 10 minutes) or the Jōetsu IC (130km past the Niigata Airport IC, about 1 hour and 30 minutes). Following ordinary roads from here, it takes 30 to 60 minutes.

To get to the southern area, get onto the Jōshin-etsu Expressway from the Jōetsu JCT. From here, exit onto the Myōkō Kōgen IC (167km from the Niigata Airport IC, about 1 hour and 50 minutes).

To get to the northern area, take the Nagaoka JCT off of the Hokuriku Expressway, getting onto the Kan-etsu Expressway. Exit at the Echigo-Kawaguchi IC (98km away from the Niigata Airport IC, about 55 minutes). It takes 60 to 80 minutes from here, following ordinary roads.

Note:

Access to the trail from any station requires the use of a vehicle- whether a private car, taxi, or a shuttle from one of the lodgings (note that some lodgings do not provide this service). Also be aware that road conditions and transportation availability will differ given the time and place, so make sure to gather this information beforehand. Additionally, since there is only limited parking available near trail entrances, it is best to use taxis or other public transportation as much as possible. For transportation availability, please check available maps.