It depends on the context:
Co byś chciał wypić? Kawę czy herbatę? = What would you like to drink? Coffee or tea?
Even though both nouns appear in a separate sentence, they are referencing "co" in the previous sentence, which is in the accusative case, as it's the object of the verb 'wypić'.
Co to jest? Kawa czy herbata? = What is this? Tea or Coffee?
This time, "co" is in the nominative case, since it's a 'to jest' construction. So both nouns take the same case.