There are over 3 dozen good places for day trips in the Kanto area - I sorely doubt you have seen them all. A few places include Nikko, Hakone, the Fuji 5 Lakes area, Karuizawa, Kusatsu, Izu, Kamamura/Enoshima, Kawagoe, Takao, Okutama, Yokohama, the Ushiku Great Buddha, Chichibu, Nokogiriyama, the Tanzawa-Oyama area, Minakami, Shosenkyo Gorge, Showa Kinen Park, and more. There are regional rail passes you can get for nearly all of them. A Tokyo Wide Pass might save you a fortune.
If you're willing to open your wallet a bit more, even more places are available - Sendai is just 90 minutes away by bullet train, and if you get a Nagano Niigata Area Pass, you can see a lot more places economically.
Same story for Nagano City - just 90 minutes or so away.
Even within Tokyo itself, there is still a lot. Probably you've seen some good city views from the Skytree, TMG, etc, but there are many more that few know about and are free.
There are a dozen traditional gardens to see also - maybe you've seen a couple, but there are some other exceptional ones that few tourists ever make it over to - Rikugien, Kyu-Shiba Rikyu, Kiyosumi, Koishikawa Korakuen, etc.https://goo.gl/tAECfM
And speaking of which, almost certainly you've already seen Sensoji, but very few people go to see the "secret" Denboin garden next to Sensoji - and it's open just 2 months out of the year - your timing is in fact perfect.https://goo.gl/q5nDom
Similar story for Meiji Shrine - few people ever discover Meiji Gyoen right in front of them as they blow past to see the shrine. Very beautiful and relaxing.https://goo.gl/MgqXu5
There is way more to fill up several more visits.