All direct flights to Japan from major cities in India are serviced by Narita Airport. If you want to use other airports within Japan, you will have to transfer at Narita Airport.
Train: The Narita Express takes around 50 minutes from Narita Airport Terminal (Airport Terminal 2) Station to Tokyo Station.
Bus: The Tokyo Shuttle or The Access Narita fixed-route busses take around 60 minutes from Narita Airport to Tokyo Station. English/Narita Airport website