You could visit the biggest Ginkgo biloba tree in Japan. It is the Kitakanegasawa no Ichou.
It has a girth of about 22m, and is estimated to be over 1000 years old. In terms of girth, it is probably the second biggest tree in Japan (after the Kamoh no Ohkusu Camphor tree).
Photo By Aomorikuma, licensed as CC-BY-SA-3.0, via Wikimedia Commons
It is near Kitakanegasawa Station, in Aomori Prefecture, at the northern end of Honshu.
There are Ginkgo trees in a lot of areas of Japan. So it depends a lot on where you want to go otherwise. Since the other answers focus on Tokyo I will just throw some answers for the Kansai area.
Osaka:
There are many Ginkgo trees lining Midosuji which is the central street going from Namba to Umeda which is a nice stroll.
There are also Ginkgo trees as well as many other tree’s such as maple in the Osaka castle garden which makes for a nice view.
Kyoto:
There are many places in the central town and around temples. Such as kiyomizu-dera.
My favorite place in Kyoto for Autumn colors is Arashiyama. You can also take the Torokko which is a train that goes through the valley where you can see a lot of foliage. Then you can also take a boat ride on the river to get back to Arashiyama
Nara:
Nara park contains a lot of Ginkgo trees as well.
While what constitutes a “best” spot is subjective, here are some popular options:
This road is located in Tokyo, between the Gaienmae and Aoyama-Itchome stations. The best time to visit is from mid-november to early december.
While this doesnt feature only Ginkgo trees, you can enjoy the view in this traditional japanese garden.
The temple grounds feature many Ginkgo trees, plus you get so visit one of the biggest temples around.
The lesson here is that there aren’t many dedicated spots for Ginkgo trees, but they are more or less omnipresent in Japan.
Visit during the end of november and you are sure to get your fill of beautiful colors.
Visit Toyko’s Shinjuku Gyoen National Garden to experience the ginko tunnel in the Meiji-Jingu Gaien, the golden canopy and carpet the most glorious in the autumn.
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