Personally I'd get out of Tokyo after a few days, but like the others I'm not sure what you like! Japan has tonnes to see, and all of it very varied. If you like the bright lights and big cities stick to them, but I think Japan is a lot more than that, there are beautiful areas of coastline and countryside which give you a better understanding of the country and its customs.
As you are going for so long, you can definitely travel right from the north (Hokkaido) to the south (Okinawa) and experience lots of things along the way. How are you planning on travelling around, most people buy the Japan Rail Pass but you would need 3 x 21 day ones perhaps, very expensive! If youre budget is not that large then you'll need to look into places you want to stay in for a while, and buy fewer passes, and activate them only when you leave a place heading to the next.
Japan Rail Pass - buy the JR Pass online