Tokyo's best examples of modern architecture tend to be fairly spread out over the city, so you're better off checking out a building here and there instead of trying to take them all in in a single day (or even a week). Here are a three of my favorites.
Tokyo International Forum, Yurakucho Station. It looks like a giant glass boat and is a fun place to just wander around in and feel small. It hosts major conventions, festivals, and concerts on a regular basis, but the main hall is almost always open.
The Nakagin Capsule Tower, Shimbashi. An example of "metabolist" architecture consisting of blockish individual apartments stacked Lego-like on top of each other. Hardly anybody ever comes here, and if the friendly manager is around he might even show you a model room.
The Audi Building, Omotesando. Glass curving at odd angles on a major shopping street. You can wander in even if you don't feel like buying a car.
Other than that, Tokyo has a wealth of beautifully designed buildings that are lurking in unexpected places--in residential neighborhoods, hidden amongst faceless office complexes, even out in the suburbs. Bring a camera with you whenever you go for a walk, you never know when you'll stumble upon an architectural gem!