For those of you unfamiliar with the geography of Japan, you may be searching to find out what the difference is between the 2 airports in the Tokyo area: Narita and Haneda.
Simply, here are the main differences.
Narita: Bigger airport with more international flight choices, but further away from central Tokyo.
Haneda: Smaller airport with less international flight choices, but closer to central Tokyo.
Narita Airport is actually located in Chiba prefecture, not in Tokyo. Transportation will take about 1.5hrs to reach central Tokyo which may sound like a bit of a hassle, however there are more airlines that fly in and out of Narita, compared to Haneda. Therefore you will have more choice in airlines, flight schedules and price.
Airport transfer is pretty easy. The most popular methods would be either the limousine bus or the Narita Express train. If you have a JR Pass, you can use the pass to ride this train. Seats must be reserved for the Narita Express, so please make a reservation prior to your ride.
Narita Limousine Bus: https://www.limousinebus.co.jp/en/bus_services/narita/index
Narita Express: http://www.jreast.co.jp/e/nex/
Haneda Airport is located within the Tokyo prefecture, so transportation can only take more or less than 30min, depending on your destination. You will have choices of the limousine bus, Keikyu train line or the monorail (the monorail doesn't really run towards the more popular areas). This airport was initially meant for domestic flights, so you will actually have more options than Narita when it comes to arranging them.
Haneda Limousine Bus: https://www.limousinebus.co.jp/en/bus_services/haneda/index
Keikyu Line: http://www.haneda-tokyo-access.com/en/
Tokyo Monorail: http://www.tokyo-monorail.co.jp/english/