The Contemporary has the easiest access to MK, while Beach Club/Boardwalk have the easiest access to Epcot through the International Gateway. If it really gets down to a decision on transportation between these two, then I'd have to go with the Contemporary as you can still easily get to Epcot using a transfer on the monorail.
My suggestion though would be to try something new. Have you thought about renting DVC points for a Bay Lake Tower stay? You'll get twice the room for half of the cost of rack rates at the Contemporary and still have access to the monorail and California Grill. One downside with a DVC stay though is that you won't get your daily maid service. You can always still pay extra for this, but most people live without it. If you consider this, you might want to check out David's Vacation Rental service, or the DVC rental boards here on this site. There are a lot of resources that may help you through the DVC rental process.
If you don't like the DVC idea, then I think that you should just stay wherever you feel happiest. Certainly balance out the cost difference in your mind, but stay where your heart tells you to go.
Good luck with whatever you decide.