Tokyo taxis are clean and reliable but expensive (initial fare ~500 yen, ~400/km). Trains and subways are vastly cheaper.
The Tokyo Metro and Toei Subway 24/48/72-hour passes save money if you're sightseeing intensively (800 / 1,200 / 1,500 yen).
Late at night (after midnight), taxi surcharges add 20%. Plan to catch the last train (around 12:30 AM).