Sankein gardens is my favorite. Relatively easy to get to from Tokyo (I believe there is a bus from the Yokohama train station) it is compact but beautiful. There is an old farm house on the property that has been conveted to a museum that is fascinating. Also, we had a wonderful tea there - green tea and bean paste cakes while overlooking the pond.

Enjoy!

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Here is a blurb about the gardens:

Sankein Gardens
A traditional Japanese garden with an area of 180,000 square meters.
Several structures within the garden have been designated as national cultural properties.
Outer garden: 9:00 - 17:00 Admission: 300 JPY
Inner garden: 9:00 - 16:30 Admission: 300 JPY
Municipal Bus (#8, 125) from Sakuragi-cho Sta. to Honmoku Sankeien-mae and 3 min. walk