If you are not going to Tokyo, don't go to NRT. Fly into KIX and take the comfortable Haruka, which goes through Osaka but continues on to Kyoto Station - total train time about 75 minutes. The Haruka is a dedicated airport connector train so it has ample luggage space at the back entrance of each car.

The only problem with KIX is the limited number of flights there. From the US, you are going to be connecting at SFO on UA. The ANA flight from SFO is a code share on the same UA flight.

I believe there is a CA flight to KIX from NYC but can't report on it.