Baseball, Soccer and Tennis I think are the most famous sports right now. There are lots of sports you can get yourself into. Basketball is not that famous though and renting a court is a bit expensive, but if you are a student there are some univ/school that has courts/club to join into.
Bowling can be found in most amusement center, like Round One. Table Tennis too. There are lots of Batting Dome too, where you can practice your swinging technique.
getting fit in japan is not a problem
