Volunteer or donate at Second Harvest.
Donate unused items such as feminine products, baby products such as diapers and lotion, items for the elderly such as adult diapers and wet sheets, as well as water, paper cups and more to the Tokyo Metropolitan Government
Donate blood through the Red Cross Society
What you can do in Japan outside Tokyo:
Make a furikomi (振込み) donation to Doraemon Charity Fund.
Donate canned food, instant rice, cup ramen, batteries, diapers, wet tissues etc. to the Shizuoka government.
What you can do both in and outside of Japan:
Donate to Red Feather Community Chest Movement, a member of United Way Worldwide, which goes toward supporting victims and volunteer groups which are responding to the disaster.
There are also many Japanese NPOs that are accepting donations and volunteers:
Even more info here courtesy of @1rick