Good Tokyo neighborhoods to stay in include Shinjuku, Shibuya, Ginza, Ueno, Asakusa, and Tokyo Station/Marunouchi. The best choice depends on your budget, preferred pace, and plans.
Before booking, check the walking distance to a station, the specific train lines serving it, and whether the hotel is near a busy nightlife street. Tokyo is large, so staying near a station that suits your itinerary can save time each day.