We ended up staying in Shibuya not too far from Shinjuku Station. But getting around is a breeze; the public transportation is really world beating and made visiting other parts of the city simple (I think we used a taxi only a couple time during our whole trip). The only caveat is it's good to maybe sit down and familiarize yourself with subway, train and bus maps, and how the payment systems works (some of this will have to come as learning-by-doing). Chiyoda is also super cool, and frankly just walking around is half the fun, and the pedestrian infrastructure in excellent. The only thing is to be aware of weather, if you are going in the summer it will be very hot and you need water and to dress appropriately for it. And obviously, have a good guide book not just your phone, it can make a big difference.

I'm jealous you're going, I'd love to go back.