Here are some of my most favorites:.
More info about this garden can be found in this useful site about parks in Tokyo: https://www.tokyo-park.or.jp/park/format/index030.html
300 y/o Tsutsuji (Azalea) Flower Garden at Nezu shrine. The shrine also got a really cool Shinto gate road (you can see it a lil on this photo's right side).
Mid April-beginning of May.
URL for info: http://www.nedujinja.or.jp/
Wisteria at Kameido Tenjin shrine. I love this flower so much! It reminds me of grapes (and I love grapes!)
The temple also got a cute bird that lives in the pond.
Ending of April-beginning of May.
URL for info: http://www.kameidotenjin.or.jp/english/index.html
Shinjuku Gyoen (Shinjuku Park) got lots of very beautiful flowers (including the ones mentioned above) and plenty of Sakura (cherry trees). URL: http://www.env.go.jp/garden/shinjukugyoen/
Sakura! Japan's national most beloved flower! There are so many great spots in Tokyo that I would need a long separate post just to include all. If I really have to name something, let it be the Imperial Palace and Shinjuku Gyoen. Some Sakura blooms in early April, some in mid April and my most favorite one blooms toward the end (of course it all depends on the weather).
May 10th-June 8th.
The one on the photo got this amazing view of Mt.Fuji in the background. It is a truly breathtaking scenery and I highly recommend it even to those who got no interest in flowers!
The 2nd location is in Saitama (and also got a view of beautiful mountains, although not Fuji-san). From April Until May.
URL with info about the one near Fuji: http://www.shibazakura.jp/eng/aboutus/index.html
URL with info to the one in Saitama: http://navi.city.chichibu.lg.jp/flower/shibazakura/
This is a peaceful garden called Mukojima-Hyakkaen. It got different flowers blooming through the year, but its main attraction is probably the Hagi (bush clover) that is very romantic to walk under.
3 Higashimukojima, Sumida-ku, Mukojima-Hyakkaen Gardens
Katsushika-ward holds a beautiful Iris festival at two parks: Horikiri Shobuen Iris Garden, which has approx 6,000 Irises of 200 kinds, and Mizumoto Park with approx 14,000 flowers of 80 kinds.
From early June until mid-June.
Sunflowers is probably the best flower out there to get you into the summer mood! The bright yellow colors against the blue sky just make me wanna jump around from happiness!
Setagaya-ward got a very happy garden of them.