The Narita Express and limousine buses indeed stop before 11pm. Were you planning on checking in the day you arrive, or the day after? I don't know how you could get around other than taxi that late in Japan, and that would be astronomically expensive if Shinjuku is your destination.
The Keisei Limited Express is a good alternate. I rode it from Narita to Ueno. You can reach the Yamanote Line at Ueno, but the Keisei station is somewhat separate from the other parts of Ueno station, so you'll have to do some walking.