There are lots of resorts in Cuba that could meet your needs. Calm water can't be guaranteed since water conditions vary with weather conditions, but some are more sheltered than others. The best bet of all is probably Los Corales (Santiago) with its protective reef and very shallow water, if you don't mind staying at a Cuban three star resort. It would help to know your budget and whether or not adults only would work for you. Melia Buenavista at Cayo Santa Maria is good, but is pricey and adults only. Time of year also makes a big difference, e.g. Jibacoa in Cuba is great in late spring and early fall, but in winter high waves and Portuguese Man 'O War can be an issue. If you don't need the "wow" factor, I have seen a lot of interesting things at Santa Lucia, and it is sheltered by a barrier reef.
If Cuba doesn't interest you there are good places in Mexico, e.g. Akumal, where you will see a lot of turtles and rays. Another possibility would be the Bay Islands of Honduras, particularly Roatan. I'm sure there are many other places, but these are the ones I am most familiar with.