First of all, let me say that we have sailed on both Oasis class (not Wonder) and Freedom class and love both. I think you will be happy with either, but strongly recommend the Independence of the Seas.
Last spring we sailed on a 4-nighter on the Independence with 8 people, including 5 and 7 year old boys. The boys had been on Disney a couple of times when younger, and we were concerned they would be disappointed in Indy. They were not. They didn't use the Adventure Ocean at all, because they were not impressed at open house. Most kids seem to love it, though They spent a lot of time at "their" pool, playing mini-golf, etc. They loved Coco Cay, but asked to go back to the ship for lunch. Our suite concierge (Carlos) was really great with them.
I would highly recommend the GS on Indy vs. balcony on Wonder, If you compare the cabins, you will see a big difference in size and comfort. Our boys (or maybe it was really their parents) needed the extra space in the Grand Suite. When the younger one needed some down-time, his mother took advantage of fee-less room service from the dining room. They ate at the table on the balcony.
I don't know if you said or anyone mentioned it, but your 3-year-old will need to be potty trained to use the kids programs and Splashaway Bay.
Keep in mind, too, that if you want to see shows on an Oasis Class ship, it is highly recommended that you make reservations. That is a problem for some. A first-time cruiser may find that overwhelming,.
Since your Indy cruise is 5 nights, there is a chance you will be invited to a mini-tour of the bridge, galley or other location, again at no additional charge. I was told they start those at 5-nights.
On both ships, Johnny Rockets is included for breakfast, but there is a charge for lunch and dinner and shakes. We tended to eat at the buffet at breakfast and lunch and the MDR at night. The servers were great with the boys, understanding that some kids are picky eaters, and made sure they got their food early.
Overall, they are both great ships, but I would recommend Independence for you