Shinjuku
The base camp that does everything
Stay on the west side of Shinjuku Station around Nishi-Shinjuku 6-chome or near Chuo Park. It's calmer than the Kabukicho side and family hotels here have proper twin rooms with space for a cot. You're 4 stops from Tokyo Disney via the JR line and 8 minutes walk to the Odakyu line for Hakone day trips. Takashimaya Times Square has a Pokemon Center, Tokyu Hands, and a kids floor. Convenience stores on every corner solve breakfast at 6am when kids wake up jet-lagged. Avoid hotels east of Yasukuni-dori. That's the red light zone.
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