Where to stay in Tokyo after 3 nights in Bay Area (for Mt. Fuji, Nikko, Tokyo sightseeing)?

Hi everyone,
We (newlyweds on honeymoon 🥳) are landing in Tokyo on 26th Nov morning and staying in the Tokyo Bay area for 3 nights. Our plan for those first 3 days is:

1 day at DisneySea

1 day exploring central Tokyo (co-ed hot spring, local food, some sightseeing)

1 day leisure/chill at hotel, maybe 1–2 attractions like TeamLab

From 29th Nov to 2nd Dec (we fly to Osaka on 2nd morning), we’re booking another hotel for 3 nights. Plan during that time is:

1 day trip to Mt. Fuji (probably Hakone or Kawaguchi-ko)

1 day trip to Nikko (happy to consider other options too)

1 day exploring Tokyo more

Question:
What area would be best to stay for these 3 nights?Looking for:

• Easy access to Tokyo Station / Shinjuku / main transport hubs for day trips

• Budget to mid-range hotels are fine (100-200$ a night)

Any advice or specific hotel/area suggestions would be amazing 🙏