Unless your flight leaves really early, why not stay in a hotel near Shinagawa, Tokyo, or Ueno, and take the N'Ex or the new Keisei train to the airport the following morning?

To do this with one transfer, btw, I presume people are proposing transfering to the JR Airport-Narita rapid train at Shinagawa or Tokyo (easier at Shinagawa). This takes a while as it can stop for several minutes in places like Chiba and Sakura to let N'Ex trains pass.