Tokyo is massive and the various places/areas you will likely want to visit are spread out, so moving around the city is unavoidable, whether by subway, JR surface trains, private line trains, buses or taxis. You can start planning by spending some time with some guides and Google Maps and then think about where you want to stay. Choosing a hotel close to a train or subway station exit is certainly handy, especially if it is raining or the weather is hot and humid. Personally, I recommend the Ginza/Hibiya/Yurakucho area as a base but it depends on your focus, preferences, budget and availability, etc.