Originally Posted by SJC1K
As much as I hate to argue with someone named after my favourite hamburger ... I can't agree. The last Narita Express leaves Shinjuku at 19:42, or Tokyo Station at 20:03. That doesn't allow for much of the evening.
I've never found the morning rush hour time to be any worse than any other time on the Narita Express--just be sure to stay near a N'Ex station, and buy your rail ticket the night before. For example, stay at the Hilton Tokyo or Century Hyatt and walk or take a very short taxi ride to Shinjuku Station. (If you take a taxi, ask to be taken to the South Entrance--say "Shinjuku-eki no minamiguchi, onegai shimasu." That minimises the walk through the station to the platform.)
And the probability of an earthquake shutting down the rail network is very small. I doubt that it happens once in five years.
I would say much of this comes down if the OP is familiar with Tokyo or not. Shinjuku station, for example, can be an overwhelming experience during rush hour for a first time visitor, especially with the jetlag kicking in. It's also a comfort issue: If I'd have a 11-12h Y flight waiting I wouldn't want to be in any kind of rush to catch it and have to worry about losing my connection. The prospect of leisurely taking a shuttle bus from some Narita hotel to the airport around 8am seems much nicer.
As for the night out, hmmm....I've done nights out in Japan after longhauls on arrival, but never with another longhaul coming up the next morning. Again, I think this depends much on the Tokyo expertise of the OP.
The earthquake thing was more of a joke, but I had one experience in 1998 when a fairly strong earthquake struck Tokyo on the morning I was leaving via NRT. Saved me the alarm clock, though.