Having seen the stratospheric prices of day tours through JTB (Japan Tourist Board) I'd recommend contacting a company I have personally used and been delighted with - albeit for an airport transfer, not for a tour.
http://www.tokyoairporter.com/charter.html
If this an option you'd like to pursue definitely get in touch and get a quote.
The charming driver we had (a keen golfer based in Shinjuku who spent time in California) spoke English fluently and proved excellent company.
(The quote I was given by JTB for the cost of a tour of Tokyo in 2006 was 52,500yen for the cost of a guide, plus 42,000yen for the car hire + costs and parking. To go to Nikko it was another 40,000 or so yen. Even back then, with the Yen being low at the time compared to USD and GBP, this was very steep - I sent the guy from Yokohama to Kyoto by shinkansen for a taxi tour with Mr Doi as this was considerably cheaper)