Hi Natalie,
How wonderful to be able to experience a Disney Vacation Club Resort with your two little ones! I truly believe that each of the Disney Vacation Club Resorts has something unique and wonderful to offer.
Disney's Beach Club Villas is a quaint resort, which I would suggest to you for a couple of reasons. First, your little ones may really like
Stormalong Bay, an amazing pool area with so much to do - including a sand-bottom area and a lazy river. Secondly, I love the Crescent Lake area upon which Disney's Beach Club Villas is situated. There is so much to explore, do, and eat, all within walking distance. You will also be in walking distance or a quick boat ride of both Epcot and Hollywood Studios. Disney's BoardWalk Villas is right across the lake, and is another great option.
You also might really enjoy Bay Lake Tower at Disney's Contemporary Resort or The Villas at Disney's Grand Floridian Resort & Spa. Both of these resorts are lovely. With children as young as yours, you might choose one of these for the quick and easy access to Magic Kingdom, if that is where you think you will spend most of your time. From either of these resorts, you can take the monorail to Magic Kingdom and Epcot. From Bay Lake Tower at Disney's Contemporary Resort, you can even walk to the Magic Kingdom!
I hope that these ideas are helpful for you, Natalie. I just do not think you can go wrong with any of the Disney Vacation Club resorts! Have a great time planning your vacation, and please do not hesitate to ask if you have any further questions.