The Ginga overnight express Tokyo to Kyoto was discontinued in 2008. It will cost a lot of money, but you still can go overnight. You'll still have to use the Shinkansen, though.
From Tokyo Station, take the final Joetsu Shinkansen departure towards Niigata, and change at Nagaoka (長岡) station for the Kitaguni (きたぐに) express train to Kyoto. The Kitaguni has unreserved standard class seating, reserved green car seating, and couchettes; all seating is non-smoking.
It is expensive.
Try using Hyperdia | 乗換案内 路線検索 時刻表 ゴルフ場 旅費精算 通勤費なら
and typing in the times you want. It should give you the options available.