Tokyo has thousands of hotels, and most “best of” lists are built from the same recycled twenty names without checking whether they are still open, let alone still good. This one is not. Every hotel below was checked against its own site, current listings and independent reviews, organised by what it actually does best rather than by star rating alone...
Tokyo does not have one obvious place to stay. It has a dozen good ones, each built around a different train line and a different version of the city. Base yourself in the wrong neighbourhood and a trip that should feel effortless turns into an hour of transfers before breakfast. Base yourself in the right one and the whole city opens up within a few stops...
Short answer: for most visitors, Haneda is the better airport to fly into. It is about 20 km from central Tokyo, 15 to 30 minutes by train for ¥300–660. Narita is about 70 km out and 50 to 90 minutes by train. Fly into Narita if the fare is much cheaper, if you are on a budget airline (Zipair, Peach, Jetstar and Scoot all use Narita Terminal 3), or if you are using a...