55 minutes by bus from Kyoto station: [K]Kyoto to Osaka(Itami)Airport | Timetable, Bus Stop & Fare | Osaka Airport Limousine OKKBUS
If money is no object, you could get a door-to-door taxi to ITM, I suppose.

From which terminal at NRT does your 5:05pm flight to the US depart?

1) If your flight will depart from NRT Terminal 1, then, the ideal domestic flight would be into Terminal 1.
ALL NIPPON AIRWAYS 2178 - Departs ITM at 1:55pm and lands at NRT at 3:15pm (which is a comfortable connection - I believe the minimum connection is 45 mins)
If I were taking this flight and checking luggage I would want to catch the 11:50 bus from Kyoto (or earlier). YMMV

2) If you depart from NRT Terminal 2, the ideal domestic flight would be into Terminal 2
JAPAN AIR LINES 3006 - Departs ITM at 14:35 and arrives at NRT T2 at 3:55pm (which MIGHT be a legal connection - but you should definitely check that with the airlines)
If I were taking this flight and checking luggage I would want to catch the 12:30 bus (or earlier). YMMV

When all is said and done, I don't see a huge time advantage to flying. As Nishimark mentioned, flying has a lot more going for it if you start in Osaka rather than Kyoto.
I feel comfortable on the trains and I like the fact that the bullet train departures are so frequent. If I miss my train from Kyoto, chances are that I'll still reach NRT on time. On the other hand, if you prefer to check in your luggage in Osaka and forget about it until you reach the USA, you might feel that flying is more comfortable.