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Yes, the Metro covers central Tokyo very well, but the stations are for the most part in obscure places. You usually have to walk 10-15 minutes from a station to get anywhere of any significance. There are of course exceptions, and the Toei lines are closer to places, but more expensive to use.
Basically, you can get everywhere in Tokyo on a 700 yen standard Metro day pass, but be prepared to do some walking as well. The JR is good if you're sticking to the loop, and it does cover most of the major places. But I tend to stay in Asakusa when I go to Tokyo, and that isn't on the JR, so I stick with the Metro pass.
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