they are non-profit orginizations that are there 100 percent to help people out with different needs (sure they also have people that work in their offices that get paid)
a yeshiva is also tzedaka to help keep it up & running although the money is going towards paying the rabbaim not poor people its still considered tzedaka.
if they were using the tzedaka money on extras like vacations C”V or unnecessary expensive computer equipment etc.. then the people in the org. buying them would be over in the sin of stealing money from YOU-not the org.-cause you gave it to the charity to help the sick person or the person stuck etc…
may you never need to use these organizations for their help