The difference between the fare class that you paid (Q) and the Y class you saw on your boarding pass is nothing. The Y simply means that you are sitting in coach, whether you are in Q or any other fare class. If you see an F on your boarding pass, that means you are in first class. So, what you see on your boarding pass is just to distinguish your class of service.
The new CO boarding passes at EWR (orange and blue) don't have a section for you class of service.