Haneda Airport is the closest airport to Tokyo City, so chances are you will be using this airport. As Tokyo is spread out over a large area, the best way to travel from the airport to the city will depend on your final destination.
For popular destinations such as the Imperial and Cerulean Tower Hotels, the Airport Limousine Bus offers a direct door to door service. These buses are ideal if you have a lot of luggage or don’t want to change trains. However, frequencies vary greatly between different service routes. For example, the Imperial Hotel bus departs three times a day, while the Cerulean Tower Hotel bus departs every hour or so.
An alternative for many travelers is the train or monorail. The Keikyu train is cheaper and some Tokyo bound trains terminate at Shinagawa, while others continue to Daimon, Asakusa and beyond to Narita Airport. It is 17 minutes from the domestic terminal to Shinagawa Station (400 yen), with trains operating between 5:30 and midnight. They run every 3 to 5 minutes, but you need to check the indicator boards carefully, as both Tokyo and Yokohama trains depart from the same platforms. If you are only going to Kamata, then you can board any train.
The Monorail takes 18 minutes and travels farther into downtown to Hamamatsucho, which will beat a Keikyu train to Daimon by five minutes. The price is comparable at 470 yen, but with the bonus of some elevated views of Tokyo Port. Japan Rail Pass holders can use their pass on the Monorail and activate their pass at Haneda Airport, though it is not very cost effective to activate it unless you are going at least another 100 kilometers that day.
If you have a lot of luggage and you do not want to pay for a taxi from the airport, or wait hours for the Airport limousine bus, a compromise would be to catch the train or monorail to the nearest station, and then a taxi from that station to the hotel. For example, a 2 kilometer fare from Shinagawa Station (West Exit) to Sheraton Miyako Hotel would be 800 yen, compared to a 5,500 yen fare from Haneda Airport. You should check beforehand which station exit you board your taxi from, as the more distant exits could add another 1,500 yen to your fare as the taxi navigates through the back streets of the larger stations, like Shinagawa. Generally the minimum fare is 710 yen for two kilometers, though some taxi companies charge a touch less. Anything longer than two kilometers, you should consider coughing up a lot more money, or travel in a group of three or four to make it cost effective.
On the other hand, if you are going all the way to Narita Airport, the airport limousine bus would be the easiest and most comfortable way to get there. The bus (3000 yen - 70 minutes) is more expensive than the train (1740 yen – 96 minutes), but you save at least one connection, and peak hour trains can be a bit crowded by the time they reach the city. While peak hour buses may be delayed by traffic jams, this is not as congested as you would think as it skirts around the city. You can also see glimpses of Tokyo Skytree Tower on the way, while with the train there is very little scenery as it goes under the major sightseeing spots in Central Tokyo. The first bus from Haneda to Narita departs at 6:25 from the International Terminal, while the last bus departs at 21:00 from the domestic terminal.
Here are my tips for a stress free trip:
• When going to Haneda Domestic Airport on the Keikyu train, check which airline you are boarding when you disembark. The JAL and ANA flights depart at opposite ends of the Domestic Airport Station exits. The back of the train is closest to JAL while the front is closer to ANA.
• The monorail is closer to the domestic airport terminals, as it has separate stations for JAL at Terminal 1 and ANA at Terminal 2, while Keikyu has the one station covering both terminals; however the difference in walking time is not material.
• Once the train and monorail stop at midnight, and the Keikyu bus at 00:40, an alternative is to take a fixed fare taxi instead of a standard taxi, with their night fares from 7000 yen. You may also consider staying at Toyoko Inn Haneda Airport, which has a free shuttle bus to and from the Airport. Room rates start from 6,480 yen for singles.
• Buses from Haneda Airport Domestic Terminal to Narita Airport operate every 20 minutes, with hourly services beginning from Haneda Airport International Terminal. If you have just missed a bus from the Haneda International Terminal, it is best to join the Narita Bound bus from the Domestic terminal, one stop away on the monorail/train or shuttle bus.