Hmm. How close to two will your two year old be? If just turning two, they'll love seeing the decorations and lights and they will enjoy the rides you take them on, but if they're closer to three, then I think they'll be more into the characters and Magic Kingdom type stuff. If that's the case, then I'd recommend a Magic Kingdom resort because of their convenience to MK.
Of the three you listed, I'd recommend BC for that time of year because of the crowds. It is very convenient to walk back to BC from two of the parks (EPCOT and DHS) and I think the resort itself has fun "beachy" decor. Also, the Cape May Cafe has Goofy along with Chip and Dale for a morning character breakfast, and little kids tend to really enjoy those characters. (The Contemporary has Chef Mickey's, so if you opt for a MK resort, that one would get my vote because my toddlers always loved Chef Mickey's.)
It would be fun that time of year to stroll around the EPCOT resorts, too, to see the decorations (which are all unique and all beautiful.) There's a bus to MK and one for AK, so you could get to those parks, too. You could also take the monorail from EPCOT and go visit the MK resorts, which are also nicely decked out for Christmas.
Of course, no one knows your family like you do.

So maybe you can make a list of what you really want to do and decide which resort based on which park(s) you intend to frequent the most. Just keep in mind that if you go during peak holiday season, it will be very crowded and it can be difficult to get around with a toddler and the 10,000 items you have to have because of the baby. LOL! (My DH used to say we had more stuff than Hannibal's army had crossing the Alps!) Whatever you decide, have a wonderful time!
-Dorothy (LadyZolt)