By plane: There are 2 international airports in the Tokyo region that usually receive all the comers (Haneda Airport and Narita International).
If your point of entry to Japan is Narita International Airport there are at least 4 ways to get to the city.
1) Narita Express (JR N’Ex) will take you right into Tokyo Station or a variety of other stations in the city like Shinjuku. It is the fastest and the best option.
2) The Keisei Skyliner will take you to Ueno Station in Tokyo but you can’t use the JR Pass in it because it is a private company.
3) There are also limousine buses between Narita and various pick-up/drop-off points in Tokyo.
4) Taxi (not recommended due to the long distance and high price)
If your point of entry to Japan is Haneda Airport there are also 4 ways to get to the city.
1) Tokyo Monorail will take you to the city for about 13 minutes.
2) The Keikyu Line runs between Haneda and Shinagawa, which is on the JR Yamanote Line and the JR Tokaido Shinkansen Line. The ride will take about 11 minutes.
3) There are also limousine buses between Haneda and various pick-up/drop-off points in Tokyo. The ride will take from 30 to 60 minutes.
4) Haneda is close enough to Tokyo to make a taxi a great option, especially outside of rush hour or on weekends.
For a short trip to Yokohama you can take a train from Tokyo station (for instance) that will bring you to Yokohama in 47 minutes.
If you come to Saitama, catch a train from Shinjuku Station that will bring you to Saitama Omiya Station in about 30 minutes.
If you come to Nagano, take a Shinkansen from Tokyo Station that will bring you to Nagano Station in about 1 h 22 minutes.
Then you can rent a car (Times Car Nagano) to explore not only the city but fabulous Nagano prefecture with its natural sights and hidden “gems”, sacred shrines and temples.