I highly recommend flying into KIX. NRT to Kyoto is not the easiest transfer in the world. If you're going the train route, you have to take the Narita Express to Tokyo Station (1 hour), then transfer with your luggage to the bullet train for Kyoto (2 hours). The fares are something like $150 each way. If you're flying from NRT, you have to re-check bags, re-clear security, fly into ITM, and then take a bus to Kyoto, which is also kind of a pain. (You'll also probably have a sizable layover at NRT since there aren't many domestic connecting flights.)

From KIX, on the other hand, you have a direct express train to Kyoto (the "Haruka") which takes 75 minutes. It doesn't get easier than that.

Another option if you want SkyTeam miles is to go BOS-???-ICN-KIX on KE. This might sound circuitous, but it's actually easier than connecting at NRT.