I’ve never worked for a government organization (well Green Fins is kind of one, but it’s a bit complicated)… I’m working for and NGO now, and I love it. But I can imagine that both have pro’s and con’s. A government job might be more steady, might have benefits etc, but it might be frustrating if your department has an agenda. An NGO relies on funding, which doesn’t always make for the most comforting living conditions, or benefits, and if the funding runs out, the project does too…
Try and do some work experience with either or both before you finish your studies, but it sounds like this year before your masters will be the thing to help you decide about your future!
Best of luck,