It's impossible to determine which nonprofits are independent. So many nonprofits are industry backed, and depend on the industries they report on for most, if not all, of their funding. Your best bet are those that have been around along time, with clear 990's that show where money comes in, where it goes out, etc. There's an organization called Charity Navigator that tries to evaluate nonprofits, and score them based on transparency, etc. Another factor that I found in my experience is when a nonprofit goes after it's own industry. For example: Find a nonprofit that attacks MLM's and dietary supplements. Just because an organization says it's an independent nonprofit does not mean it is.