We were at IOA the last week in June and it was HOT! Your 5 & 9 y/o's would do fine with plenty of liquids, sunscreen, visits to indoor attractions like Spiderman and playtime in the water areas. I would be very concerned about the baby.
Have you considered trying to go over a school holiday such as Thanksgiving? Our school usually has half days etc.. so you really don't miss much class time - even if you are gone for a whole week. We have gone to WDW just about every year at that time, once when my son was only 5 months old, and it really worked out well. My dd is now in 3rd grade and I know how difficult it is to miss school!
It is such a hard decision! Another thing you could do is make plans for you and your husband to take turns being inside with the baby, or just take him into the parks in the evening when it is cooler and the sun is not so strong. It is so easy for them to get overheated.
As for FOTL - it is the best! The parks were fairly crowded and the most we ever waited was 5 minutes! It makes touring very easy!