There are several in Tokyo.
Shinjuku Gyoen is probably the most famous in Tokyo.
It depends on the month when you are visiting Japan, but if you are planning to visit in March, you can find Sakura everywhere.
Fuji Shiba-sakura festival is very recommendable to visit from mid-April to late May. It is not locating in Tokyo, but near the Mt.Fuji, and it is only about 90minutes away from Shinjuku by bus. The contrast of pink and green on the mountain is a breathtakingly beautiful!