The Meguro river is very popular place to visit during the cherry blossom time, as you can walk all along the river with plenty of cherry trees blooming along the river.
Meguro Institute for Nature Study
A botanical garden in the middle of Tokyo. Compared to other parks, walking here feels more like being out in the forest than being in a traditional Japanese park. This is quite a good spot for hot days, as there is a lot of shade under the big trees.