well, you can't go wrong with wearing a suit. it also says that you take this opportunity seriously IMO. at least wear a blazer, even if it's not a matching suit.
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"Fashion can be bought. Style one must possess." ~ Edna Woolman Chase
Yep, I'd go with a suit. Even if you show up and you feel out of place because the rest of the staff isn't super dressed up (which is very likely), it's just a good thing to show that you are taking the organization and the job seriously. I worked at a nonprofit for a few years and it was also important to us that our candidates be able to present themselves well to donors/companies/foundations, etc.
I just interviewed and hired a few people for an internship I had open and I would recommend wearing a suit. As an interviewer and future manager to the candidates, I am always impressed when people come to the interview sessions in suits. It never hurts!