First timer - what to do in 3 days

I will be travelling to Japan (for the first time) in late September with my 13 year old daughter and am wondering what we should do in the few days we have there. We will be arriving in Narita airport at 7pm and then have 4 nights, leaving from Haneda airport around lunchtime, so 3 full days plus a bit. I would love to visit the hot baths with the monkeys with her as she loves animals, stay in a local guesthouse, then back to Tokyo to see some sights there. Am happy for any suggestions of places to see, transport options etc. Thank you! Barbara

It depends on the season that you visit.
If it is winter, you can take hot baths with monkey on covered snows.
And what the aim to trip-- for example, relax, or adventure, or feel atmosphere of other country, want to see the nature.... depends on it!

If you are in August, in Kawasaki Daishi, it is near Haneda airport,
there is local mikoshi festival.
https://www.kdtour.org/activities/5113
If you are look for " the only thing in Japan " and off the beaten track, I recommend it.
Or, if you want to go the popular place, I just recommend to go Tokyo Disneyland ( it is popular teenager, your daughter must love it!!) and Odaiba area, Team labo event.

Late September, it will be hot and possibly rainy. I'd go to Kamikochi and stay at the Onsen Hotel there. The monkeys are usually out and about. You get there via Matsumoto which has a nice castle (not sure whether that is a big ticket item for kids).

Alternatvely we recently went to Izu Shaboten which is near Ito, awesome for animal lovers.

With only 3 days I would stay in Tokyo. The monkeys are close to Shiba onsen, which would take you at least one full day as a very long daytrip to get there. When I went I did it over 2 days, which was relaxed and allowed for some other sightseeing as well.

For Tokyo, just read up the section about Tokyo and surrounding me on this webpage or any travel guide with your daughter and you both get to decide a few places where you want to go.

For Ghibli Museum (if it makes it on the shortlist) be aware how to buy tickets. You essentially need to buy them a within a few hours of them becoming available.

For Disney Land there is somewhere a crowd calendar. Others know better but crowds seem to be insane there quite often (I personally never went to any of these parks and just don�ft get it what could be nice about queuing up for an hour to then ride for a few minutes on some machine from hell...). But that�fs me.

Enjoy your trip to Tokyo!

Agree with above - stay near Tokyo.

Hot bath with monkeys (aka, snow monkeys) - the monkeys themselves are around, but there is no snow in September so they need a lot of enticement (by the park rangers) to jump into hot bath.

If you want to experience onsen hot bath yourselves, Hakone is a popular destination from Tokyo. You can visit Kamakura in the day, head over to Hakone to spend a night in a onsen ryokan, see more of Hakone the next day and head back to Tokyo.