Night buses to get to Kyoto.
There are some night buses from Tokyo Station or Shinjuku Station. It would be good if you haven't got a JR rail pass. The price is reasonable.
Also, you can choose the different type of seats. If you want to sleep more comfy then choose the 3 seater ( wide seat ) If you want a normal one take the standard seat.
You can book a seat from the link as shown below.