Tokyo is spread out, so choose a hotel near the stations and lines you plan to use. From Narita the Skyliner reaches Ueno and Nippori in about forty minutes; from Haneda the Keikyu line reaches Shinagawa in around twenty. Staying on the Yamanote loop — Shinjuku, Shibuya, Tokyo Station or Ueno — puts most sights within a single transfer.
Tokyo hotel rooms can be compact, and rooms in the mid-teens of square metres are common. Check the bed setup and look for a triple room if there are three of you. Choose the area around your plans: Shinjuku or Ginza for shopping, Disney or Odaiba with children, and Tokyo Station for an early start.
Demand and rates rise during the late-March to early-April blossoms, Golden Week and the New Year period, and popular rooms in Shinjuku and Ginza may go early. June and January to February can offer lower rates depending on the dates, which may suit an indoor-heavy itinerary.
In Japan the total can change within the same hotel depending on the plan. Before booking, check whether breakfast is included, how the public bath is used, whether accommodation and bathing taxes are paid on site, and the free-cancellation deadline. Check-in is typically 15:00 and check-out 10:00-11:00, with early check-in usually chargeable. Japanese hotel rooms are often compact, so confirm the bed configuration and whether an extra bed is possible for three or more guests.
For three nights, keeping one hotel in Shinjuku or Ginza and riding the Yamanote line is the simplest shape. If Disney is on the plan, move to the bay area for the night before to make the morning queue easier, and when adding an overnight to Hakone or Nikko, leave your luggage at a Tokyo Station or Shinjuku base.