To do your due diligence, I recommend Charity Navigator, a service that provides ratings on 5,500 charities, which has a list of highly-rated charities on its site that are engaged in the Japan relief efforts. Aside from the fact that Charity Navigator has evaluated the financial performance of each of these charities, their list also discloses which charities are committed to spending all Japan designated funds for those purposes.
And if after checking Charity Navigator's list and tips you're still on the fence as to which charity to support, then take a look at user reviews. (That's a good idea re charity in any area.) Charity Navigator has recently partnered with GreatNonprofits to include stakeholder reviews on their site. So as you examine a charity's rating, you can also see what the charity's donors, volunteers and clients served had to say about the charity's performance. And if you've had a personal experience with one of the charities, please become a reviewer and publish your own feedback thereby assisting future donors make wise choices.