I know nothing about the field, but I'll show you what I found through Google:
Tokyo University of the Arts (Tokyo Geijutsu Daigaku) has created a graduate program on animation:
http://www.geidai.ac.jp/english/film/index.html
Other universities that openly show on their websites that they have graduate courses in the field:
Tokyo University of Technology (Tokyo Ko-ka Daigaku):
アニメーション | メディア学部 | 東京工科大学
Osaka Electro-Communication University (Osaka Denki-Tsushin Daigaku):
http://www.nawate.jp/master/q/index.html
All three above are national/public universities.
A private university with such a course is Waseda:
http://wasedakawaguchi.jp/profile.html
Regarding the three that the OP mentioned:
Digital Hollywood is a new university that grew out of a vocational school, so I don't think it has expanded enough to offer graduate programs. But, it should be interesting because it's still new and also high-tech.
Tamabi & Tokyo Polytechnic are established art universities and are alma maters for many famous artists.
Link to list of universities/colleges offering animation programs (not necessarily graduate courses):
http://www.jasso.go.jp/study_j//documents/animation_manga.pdf
Hope it helps!