One of the best ways to tour Japan (Tokyo) is get on the tour bus operated by Hato Bus. はとバス
This bus has been around for a long time and now operates many tours daily and nightly. Buses are modern and very clean with a guide. You can expect spend $30 to $90 depending on the tour. If you are not familiar with Tokyo, you might want to get on it.
https://www.hatobus.co.jp