You also may come across CBO's Community based organizations, or FBO's Faith based organizations.
All of them effectively operate as charitable organizations, normally in the USA operating as 501 C3 entities enabling tax breaks for both the entity and the donor to get a tax break. But not always so do your own due diligence.
I often take a peak at Charity navigator, and Idealist to see how some of the organizations compare, but it is not a scientific tool by any stretch of the imagination. There are a myriad of organizations out there, and some will always have higher operating expenditure than others depending on the work they do. $100 may teach a hundred children for a week in India, but the same $100 will only go a little way towards treating a child with cancer just up the street in the same town.
So whilst I think charity-navigator and Idealist are good sites you cannot always try and do comparisons "Apples for apples". Each organization has its own Idiosyncrasies and operating hurdles to overcome