This site is pretty comprehensive and has links to running team sites for many universities and schools throughout Japan, some of which seem to be dead links. The Kanto region in central Japan is the home of many of the best running universities; I have added links to most of these below as well as a few strong schools from elsewhere in the country.
This article talks about an American runner's experiences training with the Yamanashi Gakuin team.
Aoyama Gakuin * Asia * Chuo * Chuo Gakuin * Jobu * Josai * Juntendo * Kanagawa * Kokugakuin * Kokushikan * Komazawa * Kyoto Sangyo * Meiji * Nihon * Nittai * Ritsumeikan * Takushoku * Tamagawa * Teikyo * Tokai * Tokyo * Tokyo Gakugei * Tokyo Kokusai * Tokyo Nogyo * Waseda * Yamanashi Gakuin
Bukkyo * Hokkaido Kyoiku * Josai * Josai Kokusai * Juntendo * Matsuyama * Meijo * Tamagawa * Ritsumeikan