If you are a non-profit with 55 employees and two business entities, would you replace Great Plains ERP with Sage or NetSuite and why?

The size and the fact that you are a NFP should not play into a tool decision.  What is the problem you are trying to solve?  What is your desired end state? Do you have the future state processes understood?  You need the answers to these question to be able to make a decision around if your current tool will fill those needs at a cost that makes sense or if you need a new one.   Switching tool costs is high, but sometimes necessary if the cost to modify configurations  (hopefully not customize) is higher than starting over.  

Ultimately, the decision should be based on a careful evaluation of your current and future needs, along with a thorough cost-benefit analysis. If Great Plains continues to serve your organization effectively, it may be best to remain with it, especially given the investment already made in the system.