In Tokyo, not in order, but the one I saw and thing are worth it.
Sumida Park (the park next to Sumida river at the level of Senso-ji : http://en.japantravel.com/tokyo/sakura-at-sumida-park-tokyo/11402
From Ichigaya station, walk on Yasukuni-dori to the imperial garden/budokan. There is nice flowers on Yasukuni-dori and on the street next to Kanda river. You can also turn right at the street just before the budokan to have a view on the moat (chidorigafuchi), and also easy access to Yasukuni-jinja : http://en.japantravel.com/tokyo/sakura-at-yasukuni-jinja/19952 and http://en.japantravel.com/tokyo/cherry-blossoms-at-chidorigafuchi/4080
Ueno park : http://en.japantravel.com/tokyo/ueno-park-cherry-blossoms2/4682
There is some nice spot along Meguro river close to Meguro station : http://en.japantravel.com/tokyo/meguro-river-cherry-blossoms-tokyo/11507
There is plenty of nice spot, so with some free time, you can see a lot of different places and enjoy sakura every day while it last.
I love the long lines of cherry blossom trees by the Tama River in Hamura City. There are more than a hundred Sakura in the place making it my favorite spot during their season.