Probably a good idea to get a packaged tour or something if you're worried about price, then you know everything is all in. I've been a few times, once on a coach tour from Tokyo to Kyoto taking in cities along the way. You can't do your own thing quite as much but it takes a lot of the hassle out of deciding what to see as they will obviously go to the famous sights and tourist hotspots.
If you choose to organise yourself, the Japan Rail ticket is a good price and gives you a lot of freedom. Taxis are a no-no, especially in Tokyo. They're very expensive.