As you won't have much time to see anything there, is a good option to take a general vision of the city, and it will take you by the city of science, whose buildings deserves a visit. You don't need to enter those museums, you won't have time to visit them properly, at least look them from outside. In my opinion the buildings itself are more interesting than their content.
Near there is located a much more interesting museum about fallas, small museum, that could be an option if you still have some hours and don't know what to see.
Apart from the Cathedral, Lonja, City of Science etc, i recommend to see the recently renewed modernist style Colon Market, in the center of the city, near the street with the same name.