One of the best iris gardens near Tokyo is hidden in Chiba, at Hondoji near Kita-Kogane Station. Every time I go there, I'm astonished anew that this temple isn't better known. It also has a superb hydrangea forest, a suitably mysterious moss garden and a pagoda that – according to the English brochure – houses "one of only a few pieces of Buddha's bone in Japan". I can't vouch for the bone bit, but I certainly enjoy the flowers and smaller shrines in the complex.
Roppongi types would be plunged into a deep depression if they had to visit these suburban wastelands, but if you love gardens, oh, you should go. It's easy to get there: take the Joban Line from Ueno and get off at Kita-Kogane. Just remember that if you're on an express train, you'll have to change to a local train at Matsudo. Alternatively, catch a Chiyoda Line train that provides a through service to Toride, and get off at Kita-Kogane. The train ride is about 40 minutes, and the temple is a 10-minute walk from the station's north exit.
You can see my photos here.
Hondoji used to be a residence that belonged to the Genji family. It was renamed Hondoji by the famous Nichiren, founding father of Nichiren Buddhism, which believes that all people have an inborn Buddha nature and can therefore achieve enlightenment in their current life. You could call it the commoner's Buddhism, as opposed to the elitist Zen or esoteric Shingon schools.
The complex has various places of interest, including a Jizō shrine, an Inari shrine and a Benzaiten temple, but its crowning glory is the iris pond and hydrangea forest. (It's really a forest rather than a garden.) Go on a weekend and be surrounded by screaming toddlers. Go on a Monday afternoon and the noise level rises even higher as gangs of senior citizens descend – they hunt in packs – and bossily order their friends to pose for group photos. The flowers are immaterial. All I want is proof that I was there ...
You can read more about Hondoji at these two (Japanese) websites, and here's another great video by AQUA Geo Graphic: