Join Date: Dec 2004
Location: Riding the rails
Programs: Japan Forum, Skyteam Elite Plus, BW Diamond Select, HHonors Gold, NWA, DL, NH
Posts: 1,936
Narita is farther out and Haneda is closer, but with those arrival times, pretty much either airport will get you into Shinjuku at roughly around midnight (give or take on various factors).
If the flight into Narita is substantially cheaper, I'd go with NRT, if the costs are about the same then HND. Taxi can be expensive but there are cheaper bus options and train options as well.