I am thinking of taking the kids to Atlantis for either fall break or Christmas break. Which would have better weather? It would either be 10/15-10/21 or 12/20-12/26. I wouldn't miss any work if we went over Christmas break, but I'm worried about it being too cold. Anyone been in these months?

Well, October is hurricane season and December can be cool in the Bahamas. The weather there is much like that in Miami or Fort Lauderdale Florida. December can be too cool for the beach sometimes, but other times it's fine.

I agree with schmerl. There would be less crowds in Oct. We went for my 40th birthday almost two years ago in October and it wasn't too crowded. The weather was also great.

The only thing is that my office will be shut down for work Christmas week, so I wouldn't miss any $ from missed work. I don't get any vacation pay. But our vacation will center around swimming, so I definately don't want to go if it's too cold to swim.

If you want to take a vacation during Christmas break and center it around swimming, I would recommend going further south. Try the Virgin Islands or Cayman Islands, ARuba, etc.
Be aware the Christmas week is the most expensive time to travel. I work in a public school and often travel during that time. It can cost twice the price you'd pay in October. It might even pay the difference for you to take days off and go in October.