Really it depends on your budget. If you want to stay on property, there are 3 levels of resort, value, moderate and deluxe. Out of the value class I would recommend either Pop Century or All Star Movies. Both have huge oversized icons, Pop Century is Pop Culture, All Star Movies is movies. Pop Century is the newest value resort and has a pop jet area in addition to the pool which is an area with spraying jets and fountains of water. The other two value resorts are All Star Music and All Star Sports. If your DC is into either music or sports then this would be the place for you.
The moderate resorts are next. At a moderate resort the decor is more upscale and lush and the pools come with a slide. Here there are 4 resorts, Port Orleans Riverside, Port Orleans French Quarter, Coronado Springs and Caribbean Beach. If you were to choose a moderate resort, I would go with either one of the Port Orleans or Coronado Springs. Port Orleans is southern themed, very pretty, they are sister resorts so you can use the facilities at both. Here you can use the pool, go fishing, go to a campfire, take a horse drawn carriage ride, rent bikes, rent a boat and in general just walk around. Coronado Springs is mexican themed and also very nice. Here you can rent bikes and boats too. It is a convention hotel though, so sometimes there are lots of adults here.
There are quite a few deluxe resorts and all of them are great in their own way. Animal Kingdom Lodge has a savannah with animals on it. You can get a room with a balcony that overlooks the savannah which is fantastic, but they are doing construction here right now and it is screwing with the animals. My fav is the beach club, it has the best pool on property (sand bottom, absolutely HUGE, has a sandy beach area for toddlers to play in). It is near the boardwalk (also a resort) where they have entertainment every night. Here you can also rent bikes and boats, etc.
Also there are about a million hotels and houses off site you can rent too.
I would also say go to the parks, at least the magic kingdom. You may be able to get discount tickets since you are attending a conference and you DC can go for free since he is under 3. November is a great time of year to go. Cool and not busy in the parks. Epcot has a food and wine festival during this time and it is fabulous. We took our DD for her 1st bday and she loved it. We are going back for a day in October and next fall as well. As you can tell we love Disney! I highly recommend www.allearsnet.com