The second location depends on what sightseeing you will do.
Certainly Ribeira Grande is bigger than Povoação, and all the places to visit there can take up to 2 days by walking, just in the city. However, the ancestral roots are not there. The nearby villages are further apart, and would take days to see all that is interesting, in my experience.
The neighboring villages near Povoação are closer to explore, such as Furnas. You could easily spend an entire day and night there. There is a lot to see by car within a 20-30 minute distance (by car) of Povoação. It takes a few hours by foot to visit the village sites, including your wife’s ancestral church of Igreja Matriz/Igreja de Mãe de Deus. My wife’s documented ancestry at this church dates back to the 1500s. If your wife needs research help, let me know. I have been researching Azores genealogy since 1986, and traveling there since 1994.
I advise you to begin your vacation in Povoação if you choose staying there, and finish in Ponta Delgada. In good weather, it will take at least an hour by car to Ponta Delgada. It does not matter where you begin your trip if you choose Ribeira Grande, about 20 minutes from Ponta Delgada.
Wherever you choose, it will be a phenomenal trip. The weather should be summer-like with lots of sunshine!