When we were there last month we weighed the VIP tour vs. doing two of the other tours. We wound up doing the Dolphins Up Close and Behind the Scenes tours.
If you are looking to get in as much of the park as you can in limited time then the VIP tour is great. You get great seats at the main shows which if you did on your own you would need to show up anywhere from 30 minutes to 90 minutes to secure; so it's really saving you some time there. You also get front of the line on the coasters and Journey to Atlantis, again, saving you a good amount of time, but if your children are not interested in those then it goes to waste. Your VIP tour also includes Dolphin, Sting Ray, and Sea Lion feedings, which would be extra without the tour, and in the case of the Dolphins, could again come with quite a wait. Sharks Underwater Grill is where the lunch takes place. We didn't dine there, but we did look at the menu, and unless your kids are really hard-core sea food fans you may not get bang for your buck there. So the theme of the VIP tour is how much time you are going to save using the tour. There is very little on the tour you can't manage on your own, but doing on your own you spend a lot of time just waiting in lines.
That was the main reason we went with the other tours. We had already spent 2 days at the park and had done most all of those things, plus our son was not tall enough for the coasters, and probably would have only ordered chicken nuggets at Sharks, so his $99 would mostly be a wash. On the Up Close Tours and Behind the Scenes tour you get to see and do things that you can not do otherwise.
Mainly because of the age of your children, I think you should weigh the benefit of the VIP tour vs. the experience you might think they might have getting to have a more personal experience with a Penguin, or Dolphin, or getting to see where they take care of the injured Manatees, etc.
For wanting to make sure you get everything in during a visit I don't think you can go wrong with the VIP, but if you are looking to spice up your overall experience, you may want to consider doing a few of the other tours.