Originally Posted by Calcifer

Do you absolutely need to get to Kyoto that day? Another option would be to arrive at Narita and arrange your tickets to Kyoto for the next morning, and then head into Tokyo and stay near Shinagawa or Tokyo Station for easy train access in the morning. You'll likely be up early with jet lag anyway, so you can catch an early-ish train and won't be missing too much time in Kyoto that way.