I visited Atlantis for the day when I was working in the Caribbean - it was fantastic. I have only heard wonderful things about the property.
The kids program is phenomenal - HOWEVER - it is very expensive. For two kids - you may get better bang for your buck with a cruise ship - as the programs are included and extra hours are very reasonable - as on, $5/hr for Late Night which lasts until 1 or 2am.
You can always visit the aquarium if you pick a cruise with that itin...maybe best of both worlds?