Thank you for your question.
It depends on the type of organization. In many cases, businesses are regulated either on the state level and/or by federal law, and in that case, some governmental entities might be the better watchdog. One example is the Federal Trade Commission, which oversees consumer protection, unfair lending, etc.
I hope this answers your question. Please let me know if you have any follow-up questions.
If the charity or ministry is BBB accredited, that would be a good organization to check consumer complaints. Organizations have no obligation to seek BBB accreditation, so it is not a broad spectrum watchdog group in that sense.
To determine how much of the charity's proceeds go to its cause, you can check sites such as Charitynavigator.org or guidestar.org.