Hibarairei,
Why those two universities specifically?
I teach at Tsukuba University, on its new Global 30 Internationalization program. Basically, foreign students can come do a full degree (biology, geoscience, economics, sociology, etc etc etc) here taught entirely in English (of course we will also teach you Japanese). As a public university, Tsukuba would be very much cheaper than either of those two you mentioned, and we are ranked higher globally. Of course, if those things are less important to you (you may have some odd onsen-fettish which drives you toward Beppu, for example) that's all good. However, you may want to consider one of the public universities' G30 programs. At Tsukuba, we have no entrance fees and first year tuition fees are waived for undergrads, saving you a million yen or more. If you are bright and willing to work hard, you might even get a scholarship.
Ours website can be found at
Degree programs in English in Japan - University of Tsukuba
Feel free to post up any questions, and I'll try to answer.