JAL, hands down.

With regards to airports I've only flown in/out of NRT. HND is definitely closer to the city center but NRT really isn't bad, there are a few train options you can hop on. Narita Express is under an hour to Tokyo Station. I believe the Keisei Skyliner is even quicker to Nippori and Ueno.

IMO in the grand scheme of things given the transit time from the US, the extra ~hour taking a train from NRT isn't a big deal.