At the first link (below) there are two sections that will be of interest for you:
- the UN system matrix, listing all organizations in the UN system
- Major groups and other stakeholders, containing also a registry of major groups organisations (many NGOs and INGO's are listed there - 3679 entries).
The third link provides a directory of UN System organisations
Permit me to also introduce the Actor Atlas which introduces the notion of social architecture (see 2nd link) and provides a partial thematic classification of organisations in accordance with their area of work ("function of government") (4th link)
Within the same approach one can then add national organisations as is illustrated for the United States (5th link)
There are at least 4.000 international NGOs registered with the UN, but to have a comprehensive list means to do serious research. The network of DRC ONGs (French acronym) listed around 3.600 when I checked last. However, I know one person who - on his own - runs four of them to make a living.