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In the 1970s, Ford introduced a glass sunroof that they named the Moonroof (actually, the American Sunroof Company, the company that made all domestic sunroofs and now known as American Specialty Cars invented it, but Ford was the first to install it). So to answer the question, a moonroof is a sunroof made of glass.

Sunroof is the generic term used to describe an operable panel in a vehicle roof which can let in light and/or air. Moonroof is a term created by Ford in the 70s, yet is now used generically to describe glass panel inbuilt electric sunroofs.
The difference is that while sunroof is the term originally used to describe a metal panel that would only allow light or air in when opened, a moonroof is a glass panel that can allow light in even when it is closed (provided, of course, you slide back that nifty fabric-covered panel to expose the glass).

http://www.diffen.com/difference/Moonroof_vs_Sunroof