Tokyo offers you the bigger Narita Airport (NRT) in the outskirts of Tokyo (Chiba prefecture) and the smaller Haneda Airport (HND) to arrive at.
Narita Airport is a huge international travel hub, most foreign flights will be arriving and departing from there. The airport is clean and belongs to the best airports I´ve ever been to, the walking distances are alright, it´s all being handled most professionally.
Depending on the daytime of your arrival, you may have to queue some time at immigration. So far, I´ve had it all: between 5 and 50 minutes waiting time, which is not too comfortable in summertime. Well, in general I´d say 15-20 minutes should be around average. They will take a picture of you and take your fingerprints before you´ll be allowed to enter the baggage arrival area. For the inspection of your luggage you should also calculate up to 10 additional minutes. The staff is polite and professional, I´ve never had any problems there. Transfer to the city can take up to 90 minutes (see below).
The smaller Haneda Airport (HND) is mainly being used for either national (e.g. to and from Nagoya, Kansai, etc.) or short distance flights (South Korea, Okinawa, etc.), but in between a few international airline companies also offer intercontinental flights to and from Haneda. It is not as crowded and busy as Narita Airport, so queuing and waiting times are being reduced a lot. The staff is friendly and polite, the airport is a role model in all regards, thus it´s not much of a surprise it´s been voted for being the second best airport in the world (Skytrax Award 2017). Due to its location, transfer times to Tokyo are much shorter as well.
Quite the oppisite may eventually be awaiting for passengers arriving or departing on the Kansai International Airport (KIX). I´m trying to avoid this one as I´ve had some negative experience several times, ranging from rudeness to chicanery, including impolite staff and mockingly dancing customs officers. Thumbs down from me for this one.
The small Kobe Airport (UKB) is worlds better in any regards. I can also recommend it, just as Nagoya Chobu Centrair (NGO). Polite staff, well kept airports, short walking distances, professional handling. Interestingly, all three of these airports have been built onto artificial platforms right into the sea at their respective city.
NARITA EXPRESS (N´EX) takes you fast, conveniently and with a touch of luxury in less than 60 minutes to the center of Tokyo. It will take you from the airport to the bigger Tokyo stations and hubs (Tokyo, Shinagawa, Shibuya, Ikebukuro), but also to Omiya, Yokohama and Ofuna.
The tickets are (one-way) 3020 Yen (Tokyo), 3190 Yen (Shinagawa, Shibuya, Shinjuku, Ikebukuro), 3840 Yen for Omiya, 4290 Yen for Yokohama and 4620 Yen for Ofuna.
Link to the Narita Express website:
You can buy a ticket for the train after your arrival, by following the train/N´Ex signs down to the train tracks.
A cheaper alternative is the Keisei Skyliner, which needs for the route from Narita to Ueno only 41 minutes and costs 2470 Yen. It also stops at Nippori, Akihabara, Tokyo, Shinagawa, Shibuya, Shinjuku, Ikebukuro and Omiya.
Link to the Keisei Skyliner website:
Optionally, there are also limousine busses waiting to take you to the city, which I personally wouldn´t recommend. Took it a couple of times but it´s not as comfortable nor fast as the express trains mentioned above.
Haneda Airport is located much closer to the city center. A monorail will conveniently take you to the city and back. The Monorail stops at the stations Hamamatsucho / Shinagawa (JR Yamanote Line).
This will only take 13 minutes and costs only 500 Yen when using a suica card.
From Hamamatsucho and Shinagawa, you can take regular trains to your desired final destination.
A word of advice regarding your luggage
I strongly recommend you not to carry your baggage throughout Tokyo during rush hour. It´s…tough. Especially when train compartments are at 300% of its capacity, you wish you wouldn´t have done it. Instead, why not save your energy and avoid stress by handing over your luggage to the baggage service at your arrival airport? It´s not expensive but convenient and reliable. They will deliver your suitcase right to your hotel.
At Haneda and also Narita and Kansai airport, there´s the 24/7 “Luggage Delivery Service Counter” or “Hands Free Travel Counter” located in the arrival lobby.
JAL ABC takes 1740 Yen for this service to get your suitcase from Narita to Tokyo. 3800 Yen for a return service back to the airport. Yamato (Taikuhaibin) offers the same service for 1800 Yen. Delivery is mostly within 24 hours (depending on the district/prefecture). I´ve used both services before, it was always delivered fast and without any problems.