Puerto Morelos vs. Negril for Family Vacation
I can't speak to the specific resort but suggest that if you are interested in off-resort activities IMHO you will have more options based out of Puerto Morelos than Jamaica. And there is a Walmart in nearby Playa del Carmen (and Cancun) in case you forgot anything for your toddler.
Relative to weather at either destination keep in mind that July is the rainy season in the tropics - expect afternoon and evening thunderstorms that usually don't last too long. Tropical storms and hurricanes are a possibility in the summer. Trip insurance is invaluable here in case you have to reschedule or cancel your summer vacation due to hurricane.