I'm not japanese, I plan to live in Japan in a few years from now, I had one or two friends from there in the past and could obtain some info that's usually hard to get if you don't know japanese. The best place to live will depend on what you're going to work, as some areas of Japan don't have the demand for some professionals.
- Why people always talk about Tokyo: it's easier to get a job there (as a foreigner), the payment is usually better (although it costs more to live there) and there's a high probability that you'll find other foreigners there as well.
- Similar, but better options, in my opinion: Kyoto (my top pick), Osaka and Fukuoka. Keep in mind that these are just the default recommendations besides Tokyo, if you're going to work with engineering/tech, these places are very good. I also recommend smaller cities (with a population of less than 1 million) as well.
If you're planning to live in Japan, I recommend you to go to the r/japanlife and r/movingtojapan subreddits, you'll find valuable information there, much better than anything I could say.