mzkfrk, it's hard to answer your question in a vacuum, since the choice of recommenders is a very strategic aspect of an application (taking into account what aspects of your candidacy you want them to emphasize, who can best position you for the career goals you're laying out for the school, etc.).
However, there is absolutely no problem with getting a recommendation from an NGO. This could offer a very nice balance to your profile potentially. It all depends on the different pieces and how they fit together.
Generally the rules are:
* pick someone you worked closely with for at least six months, preferably a year
* the work experience should have been recent, within the last three years
* this person needs to have been in a supervisory position over you - they do not have to have been formally your boss, but they need to have directly evaluated your work product
Since you're not getting a letter from your current direct supervisor, then most schools will want you to write the optional essay to explain the situation. It's totally legitimate to be getting your "main" rec from the 20-months organization, since you just haven't been at the current position long enough for anyone there to write a letter for you yet. Getting a rec from the prior employer is absolutely fine. If that rec will come from someone you worked for before (who was your supervisor in that job), then you have some leeway in terms of who to choose for your other recommendation. If you have good stories of making a strong contribution and having an impact with your work with the NGO, then that could be an ideal choice for you (again, depending on all the other elements).
Hope this helps!
EssaySnark