A fare that looks identical in economy can differ by two hours of rail and a different immigration hall. If your hotel is in Shinjuku, Shibuya or Ginza, we bias Haneda unless Narita is materially cheaper or the only nonstop.
Haneda
International terminals here have improved the “arrive and be downtown” story. Late inbound slots matter: a 21:00 Haneda arrival is a different night from a 21:00 Narita arrival. ANA, JAL, and several Gulf and US carriers use HND on routes that used to be Narita-only.
Narita
Still the right airport for many Oneworld and Star long-hauls, and for onward tickets into the rest of Japan that were built years ago around NRT. Do not plan a same-day meeting in Yokohama off a Narita noon arrival unless you like running.
Open-jaw Japan
Fly into Tokyo, out of Osaka (KIX) is a standard first-trip pattern. That is multi-city, and often cheaper than two returns. Tell us the rail pass plan; it does not change the fare filing but it stops us returning you to the wrong island.