I worked with a large number of these so called "legitimate" charities and after what I saw I will never give a penny to any non-profit. You will have far, far more impact figuring out something you care about and directly spending $100 to accomplish that than giving $5000 to any of these organizations.
In what respect did you work with them? What is your main complaint? As far as I know, top GiveWell charities give malaria nets and stuff and it saves lives at fairly efficient rates.