I recommend the service at http://www.motorsports-japan.com.

They primarily deal with car enthusiast for racing events, but it is possible to arrange a daily tour in Tokyo with them.

They charge around 500 US dollars (50,000 yen) and a native-level tour guide will take you around. If you have an idea of where you would like to go, they can plan out the itenerary for you, or you can leave it completely up to them by listing your interests (temples, shopping, "red-light district", etc.).

Or you can just do the tourist guide book thing and go at it yourself. Many people can speak English or fair enough of it in Tokyo, especially in the touristy areas. I wouldn't recommend the volunteer service unless you really want to try your luck. I'm sure they mean well, but I've heard cases where some of the volunteers' poor English is just not worth the time. Then again, I've never tried the volunteer service before personally.