You can get flights direct from heathrow to Tokyo - from experience I'd say avoid Air France and also fly direct. It's a long flight and if you're only going for 5 days you want to minimise the jet lag that will hit you on arrival. Fast train goes straight from airport to Tokyo and has several stops in the city:
http://www.narita-air...cess/train/index.html - you can choose your stop to suit your hotel location, and I'd recommend getting a cab to your hotel on the first day because you will be tired.
There's a lot to see and do in Tokyo. Public transport is excellent and cheap. Get yourself a decent city map and study it alongside a 'rough guide' or similar so you can maximise your time there according to your tastes.
If you decide to travel further afield it's worth buying a Japan rail pass in advance (see details on
http://www.seat61.com). Travel between cities on the bullet train is very comfortable.
Why not have your beach holiday in Japan too? Try this link:
http://www.tripadviso...ch_holiday-Japan.html