You can make all your dining reservations by calling Disney Dining at 407-WDW-DINE. Unfortunately you're going to have to wait a bit to make those reservations. Currently, you can only make dining reservations 180 days in advance. This has been known to change once in a while, so I'd check back here once in a while, but the 180 day rule has been going strong for a while now.
As far as your character dining options go, really any of them would be great for a three-year-old. I'd base your choice on a few factors including convenience (is there a character meal at the park you'll be visiting?), price (a few of the character meals cost a bit more than the others), and your child's character preference (different characters appear at different meals). For example, if your son likes the Winnie the Pooh characters, you should go to the Crystal Palace in the Magic Kingdom. If he likes Lilo and Stitch, you should try the breakfast at 'Ohana in the Polynesian. Mickey Mouse fans will love Chef Mickey's. You can find a listing of the character dining experiences
here.
My suggestion would be that you start with a good guide book such as the Birnbaum's guide to Disney World or the Unofficial Guide to Disney World. These will help you get a better idea about the differences between the character dining experiences (or you can ask us more questions on the Panel), and with this information you can choose the best meal for your son. You have plenty of time to think about it.