The easiest port of entry for travellers coming by bus from other parts of Japan is the new Shinjuku Bus Terminal, part of the JR Shinjuku train station complex. There is a tourist information centre on the 3rd floor and direct access to JR rail lines on the 2nd floor. Another long-distance hub is the JR Highway Bus Terminal at Tokyo Station.
Driving in Tokyo, both on the shutokō (the city's convoluted expressway network) and the narrow lanes of residential neighbourhoods, can be challenging if you are not already used to driving such roads.
If your destination is a major hotel, arriving by rental car from other parts of Japan is a reasonable option; such hotels will have drop-off lanes and parking facilities (the latter at a cost).
Guesthouses and apartment rentals are often tucked deep in residential districts that are hard to navigate and will not have parking spaces – and may be located on roads so narrow that even brief (illegal) street parking would be tricky.
Tokyo Station is the terminus for all shinkansen that connect Tokyo to major cities all over Japan. From Tokyo Station you can transfer to the JR Chūō and JR Yamanote lines, as well as the Marunouchi subway line.
Shinkansen from points west (Kansai, Western Honshū and Kyūshū) will stop at Shinagawa (one stop before Tokyo Station for inbound trains), more useful for destinations on the city's west or south sides.
Meanwhile, shinkansen from points east (Tōhoku and Hokkaidō) will stop at Ueno (one stop before Tokyo Station for inbound trains), more useful for destinations on the city's east or north sides.
Both Shinagawa and Ueno are stops on the JR Yamanote line. From Shinagawa you can also get the Toei Asakusa subway line; From Ueno you can transfer to the Ginza and Hibiya subway lines.