A short holiday has a fixed number of days, so every extra transfer inside Tokyo takes a slice out of sightseeing. Late September and early October still carry some summer heat, which makes shorter daytime walks and longer evenings out the easier pattern. Families can look at large buildings where two rooms may sit close together, while couples can pick a smaller hotel with fewer rooms. Typhoon season overlaps, so compare free-cancellation and change terms as well.
From Haneda, start with Shinagawa access; from Narita, compare Ueno and Tokyo Station routes. Shinjuku favours the west side and connections, Ginza and Tokyo Station favour shopping and shinkansen, and Tokyo Bay favours Disney days.
Narita has direct trains and limousine buses toward Tokyo Station, Ueno and Shinjuku, while Haneda reaches Shinagawa and Tokyo Station in a short ride. A mid-afternoon landing suits the Tokyo Station or Ginza side, and an evening landing suits Shinjuku or Shibuya, so the first night is not lost to transit. Over three nights, keep one hotel and treat Hakone or Nikko as a day return that avoids repacking. Plan the last day backwards from a lobby exit three hours before the flight.
Check the room type and maximum occupancy, breakfast, accommodation or bathing taxes, free-cancellation deadline and early check-in or late check-out terms in the product details.