The museum is the gem of this site, as the ruins are pretty ruined and have no tour guide or explanatory information...so you don't know what you are seeing. The cathedral is in use and St. Hermano Pedro's tomb is a revered spot for Catholics who come from all over the Americas to pray for a miraculous healing. Both are worth visiting and you are welcome to light a candle and pray at the tomb where the Saint's ashes have been put to permanent rest.
The museum (admission 5Q) should definitely be toured. The woman who was there when I went through was happy to provide information in Spanish and was quite knowledgeable about the museum's collection. Unfortunately, she only speaks Spanish. The museum has three relatively small sections. The first offers artifacts from both the original church (including an early hand written bible) and the general area, as well as collections of coins, etc. The second area holds crutches, canes, etc. left by people who have been miraculously healed by St. Hermano Pedro, along with testimonial letters and other artifacts from his intercession. The third area provides history about the Saint and his canonization. It includes a number of authentic relics -- shoes, a rosary, and a pair of the Saint's underwear. Abundant interpretive information is provided in both Spanish and English.