Spoiler Alert - Singapore wins (again) https://www.forbes.com/sites/karstenstrauss/2017/04/10/asias-best-universities-in-2017/#6ecc2be67549
My impression is that the Times Higher Education Supplement rankings are basically marketing, selling universities to prospective foreign students. National University of Singapore is a very good university, there's no doubt about that. But I'd guess that it ranks higher than its regional peers like the U. of Tokyo in this kind of ranking because it's a large English language university in a very small country. That makes it more attractive to foreign students than a Japanese language university and its percentage of foreign students is probably relatively high. It also means that more of its publications are written in English and might do better in the citation rankings.
Yeah, I always look at these rankings but they don't actually mean that much to me other than being a list of pretty good schools. Sometimes they have some sort of DL programs but the Asian universities as a whole are not very open to US/Western students. Mostly my interest is to loosely keep tabs on higher ed in different parts of the world.
That "language problem" exists in every country outside the English speaking world, even in Western countries (to some degree). However, it seems Japan has its own problems because of its demographic and economic decline: Nocookies | The Australian