If you travel on the company's dime, then I presume you value nonstop over any price difference. JAL is the only airline that flies nonstop to all three of your primary destinations from TYO, but Star probably offers the most nonstops total to those 3 destinations combined. If you pay for your own travel, then you'll want more options including 1-stops through Korea, Canada, ORD, SEA, etc. If that's the case, then I have to think that it's Star and Sky (maybe Star > Sky) with 1W distant third.
Anyways, this is not a simple question, and the airlines' hard products (esp seats), FF program quality, and routes are always in flux as we know. You may have personal preferences, favorite airline, but again things are always in flux. I'm based in SEA. I'm going with Star (put all my miles in UA) and Alaska. For a SEA guy who travels almost exclusively SEA-TYO/HKG and US-domestic, 1W makes no sense. I contemplated joining DL for a few months, but I saw that their saver award availability is horrible. In fact, it's much easier to redeem DL seats using AS miles on my DL flights than using DL miles. UA is still has decent ff program imho. AS is a great program that one could consider even if you don't live in an AS city. Problem, though, is it may be a matter of time before AS partners become exclusively Sky (if DL gobbles them up) or almost all 1W (if relations w/ DL further sour and AS can stay independent).
Credit card is an important consideration, especially for me since I probably earn >1/3 of my miles from credit card. I can't speak to card options in Jpn. In the US, UA's Chase Explorer is way superior to AS's BofA card. DL is only AmEx which doesn't work for me. If you want Chase Sapphire, then UA and KE are the only trans-Pacific airlines that you can do 1:1 point transfer with.