While Japan’s capital is huge, it’s easy to get around, with Tokyo transport one of the best public transport systems in the world.
The trains in Japan run right on time. You’ll find Tokyo’s main suburbs on the JR Yamanote Line (Loop Line), with Roppongi and Asakusa the only exceptions. This is no issue, however, as Roppongi and Asakusa are only a few subway stops from Ebisu and Ueno respectively.
Catching buses is another viable option for you in Tokyo, though trains are still preferable. If you need to get somewhere specific very quickly, or late at night and early in the morning, catching a taxi is the most convenient option.