It depends! If you are on a holiday in the mountains you might breathe deeply and say, "What wonderful clean air!" (Perhaps you live in the city and usually breathe polluted air). Or, you might look around, and say, "What wonderful clear air! I can see for miles!" They both are common and it just depends whether your focus is more on breathing, or looking.

Clean air

clear sky is correct

Clean air = the air is clean Clear air = the air has a clear color :) (not usual)