Hi Kim,
You are choosing between two wonderful resorts. They are typically fairly close in price, though check with a travel agent for pricing for your specific dates.
Disney's Animal Kingdom Lodge makes you feel like you're in Africa. Most rooms have a view of a savanna on which you might see zebras, giraffes, or other animals. The pool at Disney's Animal Kingdom Lodge is large and features a zero-depth entry, which means that you and your toddler can splash in very shallow water. Dining options include Jiko, Boma, and Sanaa, all of which offer interesting takes on African-inspired fare, but with options friendly for your children if they are not adventurous eaters. One issue that some guests have with Disney's Animal Kingdom Lodge is that it is far from Magic Kingdom Park, Epcot, and Disney's Hollywood Studios. It is very close to Disney's Animal Kingdom. The distance to the parks never bothered my family as all are accessed by bus.
Disney's Wilderness Lodge is is themed to the Pacific Northwest and a National Park Lodge. It has a nice pool and is so close to Magic Kingdom Park that you can take a boat there. You can catch a bus to the other parks. Dining includes the upscale Artist Point, as well as the fun Whispering Canyon Cafe at which you can dine on Western fare and where the servers are entertaining!
With two little boys, if they like animals, I would recommend Disney's Animal Kingdom Lodge. If being closer to Magic Kingdom Park is more important to you, and if you prefer a National Park Lodge feel, then you might choose Wilderness Lodge. I'd choose Disney's Animal Kingdom Lodge, but that's just my preference!
Please feel free to ask if you have further questions. Happy planning!