My favorite Mexican resort is Explorean, in Cozumel. Now, you should know in advance that Coz resorts tend to NOT have the "white sandy" beaches that many people picture. The all inclusive resorts on the island do have waterfront, and tend to have man made beaches.
The reason I like Explorean is that excursions off the property and to various sites on the island are INCLUDED in the fee that you pay. So, you get all food, all drink, AND one excursion per day....thinks like tours to Mayan ruins (which are interesting, but not as grand as those on the mainland), bike tours, snorkel tours (to some of the very best snorkeling in the world....this is what Cozumel is known for), etc. The people are incredibly friendly. Safe. Beautiful. Plus, the pool at Explorean is located in a jungle, so lots of shade to to be found for those who burn easily (which is me).
Check it out.
Another very nice, high-end resort on Cozumel is the Cozumel Palace. My BIL and SIL took their family there at the beginning of the month, and they loved it. The nice thing about that resort is that it offers "loft suite" rooms, with a king bed on the lower level, and two doubles upstairs. And, two full bathrooms. At that resort, you get "credits" you can use to book excursions of your choice. It has a more in town location compared to Explorean, but some see this as an advantage. All depends on your perspective.
Those are your two "higher end" family friendly resorts on Coz. Everything else is a step (and sometimes a BIG step down) from there in terms of quality, particularly in the food department.
Puerto Vallarta has had more issues lately with crime. I'd definitely look at that. Playa Del Carmen and Riveria Maya both have some amazing resorts, and of course, the big Mayan ruins. However, both have had considerable issues with sargassum on the beaches over the last few years. We are talking MASSIVE amounts, which can limit the amount of swimming you can do.