Depends on what you're planning to see. Fall can be a wonderful time to see the colorful environment around parks.... But December-January can get really cold. If I remember correctly, Tokyo historically has its coldest weather on January. If you're looking for hanami, April would be the time, but it'll be right smack into the plans of many other tourists...which would probably lead to clogged airports and full bookings.
My personal fave is just around early November. Just in time to see the fall landscape, feel a tolerable coolness in the air and see Christmas preparations=)