In that case, I'd go with the Shinagawa recommendation above. Catch a keikyu line train to Shinagawa. There's one every ten minutes or so until 23.51. Stay at one of the hotels near Shinagawa station (Intercontinental Strings is a very easy walk). Catch the N'EX to NRT in the early morning.

If you want to shorten your morning journey somewhat, you could take the monorail and a local train to, say, Ueno station. On balance, though, I think that's not as attractive as the simplicity of the Shinagawa option. (And the hotel options are worse).

Another option - Take a limousine bus from Haneda to the Tokyo City Air Terminal (TCAT) at 23.15 or 00.15. Stay at the Royal Park Hotel, which is across the road. Next morning, take another limousine bus from TCAT to NRT. I am not a fan of the bus, but it works...