There are two categories of measures: accounting-based measures and market-based measures.I will suggest using Tobin';s Q as a market based and Return on Equity as accounting based.
you can also look at social impact of the nonprofit. It is a very fashionable topic at the moment and there is lot of literature (of very diverse quality but thre you are...)
At the first glance, I would say: reputation in the media or in the social networks, number of satisfied users, social capital and links created, level of collected donations , interrnational spill-over...