Flight:
We advise you to arrive at and/or leave from Kansai International Airport (KIX, Osaka), not Narita International Airport (NRT, Tokyo). KLM, Air France, Lufthansa, FINNAIR, Alitalia, and United operate their direct flights from Europe and US to Kansai International Airport. The airport is compact and easy to use. JR trains “Haruka”, which connecting the airport and Kyoto, run every 30/60 minutes, and the travel time is about 75 minutes.
JR Train:
Shinkansen, the Japanese high speed train, connects Kyoto with Tokyo. The trains run with 3 to 20 minutes interval, and the travel time is about 2 hours and 20 minutes by “Nozomi”, which is the train with the least stops.
If your flight arrive at Tokyo-Haneda Airport, I suggest you to go to Shinagawa Station by Keikyu (Keihin-Kyuko) train and transfer to Shinkansen there. You need not go to Tokyo Station.