Only place on the list I haven’t been to is Todoroki Valley Park.

Showa Kinen Koen (Showa Memorial Park) is the one I make a point of going back to every year. Never get fatigue at this park, there have been trips where we’ve made repeated visits.

If you want to understand what it is that is being pruned and landscaped in the formal gardens, you can go to the Meguro Institute for Nature Study where indigenous flora is mostly left alone. Very central and accessible. Not on your list.

For hiking we enjoy Mt Takao - partly for spiritual reasons, but also because it is easy to get to, has beautiful paths (number 6 is our favourite) and we enjoy ending our day at the public bathing facilities at Takaosanguchi station. There is a new nature museum there now which helps understand the flora and fauna here too.

Another attraction not on your list which I would urge you to look into is the Nihon Minka En in nearby Kawasaki. Also, a self guided tour of the temples of Kamakura would include many gardens. More central to Tokyo, I would also suggest a visit to Happo-en. There are some wonderful bonsai there too (but not as stunning as the ones at Showa Kinen Koen)