Costa Maya is mostly owned by Carnival, but the little town that was originally a fishing village has a gorgeous beach. Few people bother going there, although enough go for it to be safe. But, our last time there, we each got a beach side massage. Local gals, but very good. Better than on the ship. And the water was crystal clear and just cool enough to be refreshing but not chilly. Did some shopping. I always find one really great something there. One year, a woman was dusting the shelves in her shop and it was a real feather duster, with different feathers from a huge variety of birds. She said it was not for sale, but I talked into it....for $10. Carnival keeps making it harder for them to make a living, so they are easy to bargain with and generally very friendly too. It is a short cab ride into and out of the town. They are expanding the area just off the ship into a bigger shopping complex. Prices in the ones open now are about 2 to 3 times what they are anywhere else.
Mahogany Bay is the same thing. Cruise line owned shops with high prices. I saw a fabric purse there that I had previously purchased in Cozumel for $15. It was $35 in Mahogany Bay. Not even made in Mexico. I would definitely do a tour here. Getting to the beach is awful and it is notorious for the jelly fish. Lots of people get stung. Not the fatal kind, but enough to ruin your day.
For ruins, you can go out of Costa Maya or possibly Cozumel. Just be aware that the ruins in Cozumel were completely destroyed in a hurricane a few years ago, so they will say they have ruins, but it is a mock up of what they looked like. Although it looks more like a mock up of Chichen Itza to me. Cozumel's ruins were never that impressive.
The submarine tour is not rough at all. The boat stays at the surface. I would take a meclizine (aka bonine) just in case. But, it is very tight quarters. Cozy, you could say. I would be reluctant to book this off the ship, as Cozumel is a very popular port with all of the cruise lines and this tour, plus others, can sell out.
Okay, I am finally out of ideas for you. Keep asking questions, if you need to! We love cruise talking.