I’m not sure if you can find better deal, but this one sounds like a good, no hassle, cheap way to take a trip to Japan.
I originally saw this on a blog called Ryoko Japan.
Here is a link to the deal offered through JTB.
I think you can find a way to get to Tokyo cheaper, but if you just want to lay down $1000 and have your 4 nights, 1/2 day Tokyo tour, fuel surcharge, and airfare set, this could be a good deal. I believe this deal flies out of Newark Airport so it’s good for people on the East Coast of the U.S. (West Coast people can probably find even better deals because of the proximity.)