The diving is certainly more interesting around San Carlos.
Penasco is developing at an unbelievable pace, and may turn into one of the great beach resorts in Mexico - but if it does it will be because it is close to the US and therefore easy to get to, not because it is a great dive destination. It is a very popular place for students at spring break.
All of the dive shops in Arizona organize regular trips to San Carlos - I don't think anybody is regularly leading dive trips to Penasco, although it is closer. San Carlos is the jumping off point for boat dives out to San Pedro Nolasco island, which has always been very popular with Arizona divers.