If the layover in NRT would not be very long, I would probably connect to a JAL flight to ITM (closer to Osaka and Kyoto than KIX) just because it would be easier than dealing with all of the trains with your luggage.

As far as time is concerned there really would not be a big difference. If you chose to take the train, you would take the NEX to Tokyo station, and then the Nozomi super express to Kyoto.