No Disney fan should miss DisneySea if they have the chance. No question about it. There is nothing else in Tokyo that is worth seeing THAT much (again, if you are a Disney fan).
DL, however, is mostly the same as MK. With one big exception: Pooh's Hunny Hunt. Aside from that one ride, you can miss TDL without a worry in the world. Now, one ride might not seem like such a great reason to spend a day in a theme park, but in the case of PHH, it is ALMOST worth it. Seriously, it's the best theme park ride in the world, and nobody will ever make one like it again. It cost too much money to build. They were insane for building it. They had the idea, and they didn't care how much it cost. How often does something like that happen?
It only takes one day to see each of the parks, so taking one day away from Tokyo for DisneySea is an easy decision for a Disney fan.
For our four days in Tokyo (seven days in Japan) , we spent two in the parks. The TDL hotels are too rich for my blood, so we stayed at the Park Lane Nishikasai which has a shuttle to the parks but is also at a subway stop, so it was easy visiting Tokyo from the hotel.