We ended up getting a half day tours of the major Tokyo sites using Hana Tours. I found the tour on their website, but I could not use the website to book the tour. I ended up doing it on the phone with there California office.
Except for the rain, I thought it was a good bus tour. We visited the Meiji Shrine, the gardens at the Imperial Palace and Senso-ji Temple. Enough time was left for shopping as well. The tour ran a little late so we did not get to the traditional dancing at the Visitor's center near the finish point of the tour.
There are pick up point at Tokyo area hotels, but we had to take the train from Yokohama to the pickup point.
