If you are not already, start looking at Waseda. The criteria that you mentioned, i.e., courses available in English and an East Asian studies program narrows the field very very significantly. Sophia university has a global studies program that offers English classes and covers some of the material you are talking about.
I plan to study a similar subject on a monbukagakusho scholarship that I should be receiving for this upcoming fall, and and those were the only two schools I could find that offered asian studies and English/Japanese.
You may want to look at that university called something like 'international university'--I believe that has similar courses, but they will only be in English (no Japanese classes), so that was a deal breaker for me. Also the location...
Ritsumeikan-Asian pacific university might be another option...
As far as reputation, both nationally and internationally, there will probably be a big dropoff after waseda, so keep that in mind.
If you want to study at any of the other top universities, you will have to have very good Japanese (1kyuu level, or almost on par with the Japanese students)