I’ve been to Tokyo a couple of times, once was staying with a friend who is way off in the far flung suburbs, and once was more central in an area called Ueno. Ueno is a good spot, but from what I’ve seen in Tokyo if you can stay in one of the central prefectures, it doesn’t matter where you are. They’re all very well connected. I don’t remember the name of the central prefectures, but Shabuya is one, so is Tashima and Shinjuku.
@darwink is very correct about the Yamanote line, if you can stay somewhere near it you’d golden. Ueno has a Yamanote station.
One important note I should mention there is more than one Metro operator in Tokyo, JR rail and another operator. I think it’s called Tokyo Systems or something like that. A ticket on one system isn’t transferrable to the other system, so make sure to Google buying a a pass that works on both systems.
You’ll really like Tokyo, and to be honest as long as you’re staying somewhere fairly central you can’t go wrong. You’ll have easy access to all the interesting places.
I recall that hotels were more expensive in Shibuya and Shinjuku, but it might depend on the time of year.
Also, another important note if you’re going to Japan, specifically for cherry blossom season, be aware that it is very busy and more expensive, and also the time the blossoms are in full bloom at different times of the year, depending. One of the times I went it was mid April and the blossoms were already done.
Oh another thing, don't be afraid to use the street vending machines. They are surprisingly good, but maybe google which ones are the best. My friend knew all the good ones.
Me and my son are planning to go to Japan and Korea this year. Plan so far is to fly to Tokyo, spend about 10 days in Japan, fly to Seoul, spend a few days, and then fly back directly from Seoul.
