bugster88

Thank you @EAstudies and @potsupotsu for your kind responses. It's given me a broader perspective from which to consider this: what kind of work do I want to do; what kind of scholar do I want to be? Thank you for reminding me of these questions. My stay in the US does not have to be permanent, but the training I receive at a US institution would indeed greatly influence my future prospects and capabilities as a researcher.
Now to weigh a US Ph.D. program against secure employment in a country with healthcare relatively figured out...a whole different sort of problem, haha.

Just my personal opinion:
The U.S. is indeed in a precarious state, to put it generously. Nonetheless, I don't think the U.S. will completely "eat itself" in the next six or seven years to the point academia will also collapse. Major U.S. schools have large endowments compared to schools in other countries due to how they operate the schools, and they still have influential scholars, resources, and research networks here. State schools are indeed more dependent on the government grant, but if you're a student from the U.S., I don't think your stipend will be affected any time soon. And regional studies like EALC/EAS are not an exception.
If any, after doing a Ph.D. in the United States, you can be a professor in another country. Every year, there are quite a few Ph.D. recipients who get a tenure-track job in Japan, South Korea, Hong Kong, etc. This is a very common practice. However, the other way is simply not an option. There are numbers of scholars who have a B.A. or M.A. from East Asian schools, but all of them (or at least I haven't seen a single exception yet) have their final degrees, i.e., Ph.D., in the United States. This sounds unfair since this is East Asian studies, but this is the reality. So you should consider where you'd really like to stay after graduation. If you are sure that you only want to stay in Japan and nowhere else, then U Tokyo is a great option. But if you seriously want to remain in academia and do not work in an industry, a Ph.D. degree from the United States will open a bigger academic job market for you, and this includes moving back to Japan.
Lastly, you should remember that methodologies and the academic trend may differ in the United States and Japan. Even if you're studying the same discipline, let's say Japanology, the U.S. schools are becoming more and more inter-regional and interdisciplinary (though in varying degrees). Also, grad schools here and there have different cultures or vibes (e.g., a relationship between a grad student and professor), so that would be another thing to consider. 
And congrats on your acceptances!

Yes, I'd echo what @EAstudies said. I'm not an American citizen myself, and I definitely agree that the situation in the US seems incredibly scary, but remember that the current president is fairly unpopular and the election is coming up soon, so you will very likely not have to experience this for the entire 6 years you spend in graduate school in the US.
Also, while Toudai is a great school, keep in mind @EAstudies point about the way a foreign degree will be looked at in the US. I'd also encourage you to think about the way the training you will receive in Japan will be perceived in the US because there are major differences between Japanese-style scholarship and US-style scholarship. Japanese historians, for example, tend to produce works that are very descriptive and focus narrowly on a particular subject or particular documents, while in the US you will be encouraged to make a more analytic "big picture" argument. Both styles have their positives, but it might be difficult to make a name for yourself in the US if you produce Japanese-style work.