We've stayed at all the MK resorts except for the GF. I would recommend them all to you. Look at prices and themes and decide what most appeals to you-- I don't think you will be disappointed by any.
The Wilderness Lodge is where we stayed our first three trips-- when our kids were the youngest. The boat that goes from the resort to the MK was really convenient. You can wheel your stroller right on board, baby asleep inside. You can also take a different boat to the CR for a meal or to hop on the monorail to the TTC/Epcot (it was more "fun" for the kids than taking the direct bus LOL). You do have to fold up the stroller for that boat. The pool there is pretty and the kids love the geyser. Lobby is exciting for kids, too. They have a great Hidden Mickey list. I am not crazy about the food choices-- never have been a big fan of Whispering Canyon Cafe (smoked meat smells/flavors aren't my thing LOL). For me, the WL has the most cozy, special feeling. It's still my favorite resort, by far.
The Poly is really pretty and has a great pool, too. I like the restaurants a lot-- Kona is a great breakfast spot and O'hana is yummy for dinner. It feels relaxed. My kids love the beach area, and it is great to watch fireworks from there. It is pretty large and spread out-- and if it's raining it can be a hassle to get from your room to the main building. Depending on which longhouse you're in, it can be a pretty far way to walk to the TTC. However, staying on the monorail line is super nice!
We tried the CR last trip and we were all blown away by how convenient it seemed compared to everywhere else. The monorail going through cannot be beaten in terms of convenience! We visited Epcot more than usual because of that.

We found the bus service to be the best here (though it may just have been lucky timing). The walkway to the MK is awesome, especially at night when the monorail line is huge. The pool isn't really "themed" but it's still pretty and my kids enjoyed it. Their favorite thing about the CR (besides the monorail) is the gameroom. When we were there, the counter service restaurant was this temporary "Grab N Go" which was honestly horrible. However, that's gone now and the new place is open. Reviews are good. We all enjoyed the California Grill.
Good luck deciding!
