Tokyo is the main entry gate to Japan. The city has two airports, Narita for international flights, and Haneda for domestic flights. The best way to get to and from the airport is by the Narita Express train. Airport taxis should be avoided because of their high cost.
If you want to visit other cities in Japan, you can fly or move around with the Japan bullet trains, the Shinkansen. If you are going to visit several cities, I recommend buying the JR pass, which gives you free rides on most Japanese intercity trains.