Well, I've only traveled JAL on domestic flights and once Tokyo-Beijing (so no lie-flats in biz), but the service has always been impeccable.
Regarding transfer from NRT to the center of Tokyo, I guess it depends where you are going. Most large international hotels are served by
Limousine Bus, and this is my preferred method of travel. If your destination is not on their routes, Narita Express train is fast and relatively cheap.
As for hotels, I've found both Hilton Tokyo and Intercontinental ANA to be quite nice, and pretty good with upgrades.