It really depends on how you want to move around in Kyoto and around Narita. The bullet train would worth the most value if you buy a pass, but buying that pass and only use it for the NRT-Kyoto journey might not be worth it. I would go to this site called jorudan as it's the best tool I've found so far(use google translate). And if routes far enough like yours, they'd sometime suggest domestic lcc, which I search for prices here.

BUT, be aware that if you're going to Kyoto by flight, there's another 90 minutes train ride from KIX(near Osaka) to Kyoto. So yes the train might be a better option. Since there are a whole lot of different train types in Japan, I'll stick with Jorudan for figuring out the best routes to take the train, and it's easier to show the staff for purchasing tickets.