Assuming you'll be wanting to spend most of your days at MK, I'd go for VWL as they have both a boat that goes to MK (our DD5 loves it) and now a direct bus. We like VWL because it's cozy, a bit quieter than other resorts (which is good for us after being in a park all day), has its own pool and hot tub (although all guests at WL can use them both, most opt to swim in the main pool with the slide), and is a fun place to just explore--totems, a geyser, hidden Mickeys, and a path to FW that's good for biking, walking, or running. There is a boat and bike rental right behind the quiet pool, as well.
Some complain that VWL doesn't have a lot of eating choices, but we found the Roaring Forks grill to be just fine for fast food type items and drinks. For sit down service, you have Whispering Canyon Cafe which most people love with its rowdy behavior and all-you-care-to-eat meals--personally, we didn't much care for it. Then there is Artist Point, one of WDW's best and nicest restaurants (yep, kids are welcome, too). Since the suites at VWL have full kitchens (studios have kitchenettes), we usually eat breakfast in the room and often pack lunches. Seeing as you'll only be there for two nights, I don't think eating options will be an issue for you, anyway. To us, VWL is home away from home. Good luck on your choice.

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