Hi Jodi,
Welcome to the Moms Panel! If you're looking for a beautiful day at the beach - you really can't go wrong with either excursion. If you focus is more beach, swimming and splashing - I would probably opt for the
Blue Lagoon Island Beach Day because this is within a cove that will be more calm and serene, which is perfect for the little ones. Although the beach at Atlantis is amazing, when I was there I found the surf to be quite rough and it was very windy, as there is no protection from the open water.
If you're looking for a little more than the beach, the unique aspect to the
Atlantis Beach Day is that you are granted access to the Dig, which is their their amazing aquarium and wildlife habitats. This would surely be spectacular for the entire family. Although Blue Lagoon doesn't have an aquarium, they afford you the opportunity to watch the dolphins and sea lions at their encounters lagoon.
The other important factor is that you the Atlantis Beach Day is a bit more flexible on when you can return to the ship. Busses will depart approximately every 1/2 hour, whereas with the Blue Lagoon you have your choice of two return times.
Now, just to add one other option - our favorite thing to do in Nassau is simply stay onboard. This is the perfect opportunity to give the kids the run of the pool while most guests disembark in Nassau. Castaway Cay gives us the beach day we crave while on our cruise vacation (without the added excursion expense), and the kids really enjoy the uncrowded amenities onboard while we are in port.
I hope this helps, good luck with your decision!