Though most international visitors will use Narita International Airport, there is a second airport in the Tokyo metropolitan area that is mostly used for domestic flights, though there are limited international connections, mostly to other Asian countries. Haneda Airport is a good choice for going long distances in Japan when you do not have time for extended train travel.
Flights in the off season can be very competitive to shinkansen rates if you do not have a JR Pass. If you are planning to go to Hokkaido, Kyushu, or Okinawa, consider looking into the option of air travel.
The airport has two terminals connected by a free shuttle bus. Terminal 1 airlines include JAL, Skymark Airlines and Star Flyer (servicing Kitakyushu and Fukuoka Flights) and Terminal 2 airlines include ANA, Air Do, Solaseed, and Starflyer (servicing Kansai Flights).
The complex is barrier-free and has most of the facilities you would expect from an airport: a bank and foreign currency exchange, post office, baggage storage and delivery, restaurants and duty free stores. There is also a clinic and barber shop. Haneda Airport is served by many bus lines throughout the region.
It can also be reached by the Tokyo Monorail from Hamamatsu-cho Station or the Keikyu Airport line from the Keikyu Kamata Station in Tokyo. For information about the domestic terminal: http://www.tokyo-airport-bldg.co.jp/en/
For information about the international terminal: http://www.haneda-airport.jp/inter/en/