Being at Atlantis a couple of times, I would have to agree with this. Atlantis is probably better for kids (more to do, likely more kids, can go other places like the market in Nassau), but will definately be more $$$. Food is not cheap at Atlantis.
Cruise ship would likely be easier and less expensive. You may want to check into the Disney cruises as a more kid friendly cruise. They have a private island that they go to.
Not sure if it is an option anymore, but you used to be able to stay across the street from Atlantis at the Comfort Suites for less money and still use the Atlantis facilities.