Narita Airport (Tokyo) Express trains and buses run frequently to central Tokyo (around ¥3000; one to two hours) between 6am and 10.30pm. Taxis cost ¥20,000 to ¥22,000.
Haneda Airport (Tokyo) Trains and buses (¥400 to ¥1200, 30 to 45 minutes) to central Tokyo run frequently from 5.30am to midnight; times and costs depend on your destination in the city. There are only a couple of night buses. For a taxi budget between ¥6000 and ¥8000.
Kansai International Airport (Osaka) Express trains run frequently to Kyoto (from ¥2850, 75 minutes) and Osaka (¥1430, 40 minutes). Buses cost ¥1050 to ¥1550 to central Osaka (50 minutes), ¥2550 to Kyoto (90 minutes). Trains and buses stop running close to midnight. A shared taxi service to Kyoto costs ¥4200; a standard taxi to Osaka starts at ¥14,000.