If you do Atlantis with an excursion or on your own it wont even take 1/2 a day. Do it in the morning and either have lunch there or go back to the boat for lunch. Then you can easily walk to the pirate museum. It is a large purple building located behind the straw market. You will have to walk 2 blocks up, behind the straw market, you cant miss it and it is a good museum. Well worth the $12 per adult it costs. It took us about an hour and 15 minutes to leisurely go through it. There is a lot to read, so it takes a little while to go through. It is self-guided, so you go at your own pace. You can easily do both and even have time for a horse drawn carriage ride by the port on your way back to the ship. $10 per person, about 25 minutes long.
mom x4,grandma x4