"Freedom House and the National Endowment for Democracy stress their commitment to freedom of thought and democracy, but both cooperated with a CIA-organized propaganda operation in the 1980s, according to documents released by Ronald Reagan’s presidential library.
One document showed senior Freedom House official Leo Cherne clearing a draft manuscript on political conditions in El Salvador with CIA Director William Casey and promising that Freedom House would make requested editorial “corrections and changes” – and even send over the editor for consultation with whomever Casey assigned to review the paper."
http://www.commondreams.org/views/2015/01/09/cias-hidden-hand-democracy-groups
"Since its founding in 1947, the CIA had been deeply involved in secretly funding and manipulating foreign non-governmental voluntary organisations.
These vast operations circled the globe and targeted political parties, trade unions and business associations, youth and student organisations, women's groups, civic organisations, religious communities, professional, intellectual and cultural societies, and the public information media. The network functioned at local, national, regional and global levels.
Over the years, the CIA exerted phenomenal influence behind the scenes in country after country, using these powerful elements of civil society to penetrate, divide, weaken and destroy organisations on the left, and indeed to impose regime change by toppling governments.
Such was the case, among many others, in Guyana, where in 1964, culminating 10 years of efforts, the Cheddi Jagan government was overthrown through strikes, terrorism, violence and arson perpetrated by CIA agents in the trade unions.
About the same time, while I was a CIA agent assigned to Ecuador, our agents in civil society, through mass demonstrations and civil unrest, provoked two military coups in three years against elected, civilian governments."
http://www.informationclearinghouse.info/article4332.htm
The list goes on and on. While the funding for AID, NED and other NGO doesn't come from CIA, there is plenty of evidence in CIA coordinating and directing these organizations in conducting covert activities abroad.