getting around

Hello, we will be staying in Tokyo for a few days and visiting various neighborhoods within the city as well as making several day trips out. Would it be more convenient to find a hotel near the Shinjuku station or the Tokyo station? It seems that these are the two largest hubs for transportation, but I'm not sure if one is more convenient than the other. (Some of the places we plan on visiting while staying in Tokyo include Ikebukuro, Shibuya, Ginza, Odaiba, Harajuku, Asakusa, Kamakura, Yokohama, and Nagano.)

Also, I'm debating whether or not to purchase the JR Pass. We will be traveling beyond Tokyo on the last leg of the trip, but how handy is it within Tokyo itself? I read that the pass is not valid on subways; is it feasible to get around Tokyo on JR lines alone?

Thanks for the help.

I can't answer all of your questions - but I can tell you that you can't ride the subways in Tokyo with a JR pass.
There are JR lines that can get you around, and the cost of the pass has to be compared to the price of the fares of the day trips you're planning - but for me, the biggest consideration is usually not so much financial (unless its in the hundreds of dollars) but for convenience. If you buy a SUICA or PASMO card, you can put in whatever amount of money you want, and then hop and off any lines in Tokyo. You can add money to the card as needed. Subway fares are cheap. To me the convenience is worth using one of these cards.

Really Tokyo is so well connected by subways and trains (I'm sure you've noticed that the subway map looks like an explosion in a spaghetti factory!) that pretty much anywhere in central Tokyo is well connected, and you could be in Shinjuku or Tokyo in 15 mins or so.

Shinjuku and Tokyo are two very busy, potentially confusing areas- it might suit you more and be simpler to stay in a slightly quieter area (Akasaka, Asakusa etc.)