American Red Cross
NY Japan Society - your state may have a donation drive open as well, so check if you'd like to get involved through a local institution!
Second Harvest - if you are currently in Japan, consider donating very much needed supplies/food.
As I said, you can get in touch with your state's Japanese embassy for information to see if they are doing any local drives, fundraisers, etc. NY's Japanese embassy has posted information about the Japanese Red Cross Society, which will put your donation directly toward "the affected population of the earthquake and tsunami". Please see the site for all the details.
A lot of people worry that their money may not go to where it should. These worries are valid - there are 最低なpeople in even these times - so if you are one of those people who want to make sure you aren't hoodwinked out of donating to the victims of the disaster in Japan, check out this site. The American Red Cross (link above) is definitely one that can be trusted.
Keep informed with NHK's live broadcast.