I work at a non-profit college. I think non-profit colleges are sometimes a hybrid of the non-profit and for-profit worlds, since they are non-profits and it definitely shows in how they're run, but there's also aspects of a more normal company in that they are providing a service for a fee and people sometimes see them more as a corporation than as charity. So, with the caveat that I'd consider my non-profit to probably not be typical of all non-profits…
No one in the upper administration here has an MPA, but I have heard them discussed. I'm the Controller here; my direct manager is the CFO/VP of Business and Finance. I'm a CPA; he has his MBA. We have 2 other VPs; one has his MBA; the other has an MA and MLS (Master of Arts and Master of Library Science?) and a PhD. The one with the PhD is the VP of Academic Affairs/Dean of the College. Our President has a Masters in Education and a PhD in Philosphy, History. However…my impression is that the MPA is a more up-and-coming degree. While it may have existed for awhile (I'm not sure), it seems like it's gaining traction more in recent years. So, since the upper administration here all earned their degrees many years ago, the MPA probably wasn't a common option when they were earning their degrees, but it may be that it will be common for administration of a similar level in 10 or 15 years, which would be the people earning their degrees right now.
Since I work at a college, degrees are discussed a decent bit. From the discussion I've heard, my impression has been that the MPA is like an MBA, but with less accounting/finance focus. My understanding is that the reason it's thought to be better for non-profits is because knowing how to create a profit isn't as necessary for a non-profit, so having less accounting/finance focus is OK for non-profit management. So, since you've already got the CPA to demonstrate your competency in the financial side of things, the MPA might be a fine choice for you to complement the CPA and show that you're competent in the non-financial aspects, too.
Just be aware that the MBA degree is still much more well-known, especially outside of the non-profit world. So, if you decide after another couple years in non-profit that you'd rather work in a for-profit, then the MPA probably won't be nearly as useful as an MBA. However, it won't be un-useful.
Personally my goal was to complete an MBA, even while working in a non-profit, unless the college I worked at began offering an MPA (and not an MBA), and then I'd pick the MPA simply because I could take it for free as an employee. So, by that logic, if I was in your shoes, I'd probably do the MPA since it's free. However, I think the benefits of the MPA probably won't be as great as those of an MBA.
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