SAN-LAX was cancelled during the pandemic, that’s the reason for the routing via PHX or DFW. I’d pick JAL over AA any day except I believe the SAN-NRT flight still has angled flat business class seats. They’re not great.

HND is closer to Tokyo proper so is usually preferred. NRT isn’t really bad, just a bit more inconvenient. I’d say your best option is to try to get a JAL flight from a different gateway than SAN that has lay flat seats, followed by the AA options via DFW or PHX/LAX with SAN-NRT being the last choice. You’ll have better lounge options at LAX or DFW as well.

For me comfort of the seat would take priority over the Tokyo airport as it’s a minor inconvenience to fly in/out of NRT. I’d prioritize being more comfortable for the 10+ hour transpacific flight than the 45-60 minutes saved by flying into HND.

Edit: Looks like JAL is flying SAN-NRT with lie flat now, In that case I’d go with that. The lounge at SAN is pretty basic but not worth going out of your way to DFW or PHX/LAX for their offerings. Unless SAN-LAX comes back and you could get into QF first lounge if it reopens. Salt and pepper squid might be worth that detour.