Looks like Pop Japan Travel has competition because Media Factory is now offering their own tours, aptly named Media Factory Tours. So far, they have two tours listed at their site, the first called Escape to Tokyo 2010 Tour and the second Escape to Kansai 2010 Tour. Both tours are priced the same with the full fare (i.e. includes air fare), setting you back $2495 USD but if you prefer to book your own airplane, you can knock off a thousand dollars with just $1495 USD for the land tour alone.
That may sound a bit steep but considering you get all the following below, it seems pretty reasonable:
* Round trip flight LAX-NRT
* 6 nights hotel w breakfast*
* Limousine bus between NRT & Hotel
* One day full sightseeing bus w/English speaking guide
* 4 days JR tickets
For those living further from Los Angeles, you will have to put in more for air fare to make the connected flight or maybe it would be best to buy your own plane ticket to Japan. If you do buy your own plane tickets, I highly suggest taking JAL or Korean Air. The food is excellent with a mix of Korean/Japanese fare with standard western food choices for the non-adventurous eaters.
For more information on these tours, drop by Manga Factory Tours.