If you are based in SFO and travel to Tokyo frequently, my recommendation is either UA or JL. UA has a lot of flight options from SFO to NRT (i.e., two daily direct flights to NRT, connecting flights through LAX and SEA) and also SFO is a hub airport for UA, which makes it convenient for you to fly pretty much every where within the US. If you don't fly domestic too often but just SFO to Tokyo, JL may be a good alternative for you since their award or upgrade availability and miles required to redeem arwards are very generous compared to many US based airlines.

The only reason why I am stuck with AA is that I need to travel to DFW often. If you need to travel to DFW often, AA probably is the only choice.

I hope it helps.