I've done both, the Atlantis and a cruise, and my suggestion for you would be the Atlantis.
At the ages your children are at now, the Atlantis will charge them as children. Once they hit 12, you will be charged an additional $45 per child per night for accomodations, and an additional $29 per day for the MAP or $42 per day for the Gourmet dining package. The dining packages are a MUST at the Atlantis, and must be taken by all members of your party. These prices are before taxes and gratuity and will really add up fast. If you really want to go there, I would do it now, before the kids fall into that 12 and above range.
The cruise will charge your children less as 3rd and 4th persons in your cabin, regardless of their age, even up to 18.
If you have a 5th person with you (either another child or a grandparent/nanny/friend) you will have to get 2 rooms at the Atlantis. Good to know in case you are thinking of adding to your family
For these reasons, unless cost is absolutely NOT a factor for you, I would go with the Atlantis this summer, and do a cruise for your next vacation.
I see that you were looking at a shorter Disney cruise, which is good, because Disney is NOT doing the 7 day cruise from the Florida port this summer, having moved that boat to California for Mexico cruises.
Honestly, I would say that the 7 day Disney cruise is a much better value all around than the 3 or 4 day Disney cruise, and you will be able to do 7 days again from Port Canaveral next year.
I don't think you'll be disappointed either way....a cruise is an excellent value with children, and the Atlantis property is beautiful and has tons of activities for the kids. Expensive, yes, but it will be a memorable trip.