There are very few evening flights at NRT (if any) and the buses cater for the flights, not the airport itself or the town. Don't expect to find much open if you arrive there late, it's pretty dead by 9pm.

When staying in Narita I prefer to stay in the town itself rather than in one of the 'satellite' hotels which require you to take a courtesy bus or a taxi (hotels with convenient locations are the Mercure, for two, or the Comfort Inn, for one). This allows you to take a train from Ueno or Nippori right up until 11:30pm. The Mercure is just a few steps from Narita Keisei station (no stairs) and although there is a courtesy bus available, the train from here to the airport is so convenient and fast I've never used it.
The other benefit of staying in the town is that you can explore Narita at night (the nightlife isn't at all bad there) or early in the morning, so your vacation only ends once you check out of the hotel and get the train/bus.

In the past I used the Tobu Holiday Inn at Narita, but this involves getting to the airport (last train from Ueno/Nippori arrives just before 11pm, the last NEX just after 9pm) going through the airport and then waiting for the courtesy bus there (or getting a taxi - around 1,000yen). At this hotel there is NOTHING. Even the nearby convenience store is no more.