Why pay a pricey tour guide when you can have an enthusiastic, English-speaking local show you around Tokyo -- for free?
Tokyo Free Guide is a nonprofit organization made of up volunteers eager to introduce international travelers to Japanese sights and culture. They make an introduction to Tokyo easy (especially for travelers nervous about navigating a foreign city), building itineraries around what you want to do.
Visitors who have used this service rave about the personalized approach it provides -- as do respected publications such as The New York Times and Washington Post. When requesting a guide, just indicate what you're interested in seeing and/or learning and how many days you'll be in Tokyo. You'll get matched up with a guide, and can even begin corresponding over email ahead of your trip.
Note: You are expected to pay the costs of the volunteer's meals, admission fees and transportation costs. No tips are necessary, but they are always appreciated.