Taxis are the most expensive method for traveling around the city, especially from the airport to your hotel (approximately ¥20,000), and, because of heavy traffic, not necessarily the quickest. Taxis can also be small, which can cause problems for travelers with large amounts of luggage. The advantage of a taxi is that you will be taken directly to your hotel. After a long flight, this might be worth the large cash outlay.
Taxis from Haneda Airport run closer to ¥6,000.