Another oft-ignored (in guidebooks) garden lies just east of Hamamatsucho Station. Kyu Shiba Rikyu Garden is small, but has some beautiful rocks, nice decorative trees, and a pleasant lake.
The garden boasts a large number of landscape rocks, plus lots of stepping stones across the fields and over the water. There's also a couple islands, one of which is inaccessible, and a small mountain that gives a great view of the entire garden.
If you have a short time in Japan, you'll probably want to go to Koishikawa Korakuen, which I consider to be the most beautiful garden in Tokyo. But for residents or garden enthusiasts, it's worth an hour or two of your time.
The garden is open from 9:00 AM to 5:00 PM (closed around New Years), and admission is only 150 yen.
Here are the rest of my photos from my visit last year: