I am deciding between Munk and NPSIA also.
I am leaning towards Munk because it definitely keeps more career options open for you. The majority of Munk grads go into the private sector but you can also go into the public sector if you decide. If you look at the courses at Munk (i.e. Financial Management for Global Organizations, Capstone Seminar) there are many which are both global affairs and business oriented and make you more marketable for the private sector (i.e. consulting). With that said if you know for sure you want to go work for the government, especially the federal government NPSIA is probably the better option with their co-op and connections to Global Affairs Canada.