I've found that the WalMarts in the WDW area usually sell the Sam's muffins. They come in 4-pks instead of 12, and they are a bit more expensive than at Sam's, but if that's your only reason for going there, it will save time.
Publix' bakery also has some decent mega-muffins. I got some praline-pecan muffins a while back that I really liked and that kept very well.
On short trips, we carry down the muffins in a tupperware-type container. Carrying them frozen also works to keep them from getting squashed.
We refer to Sam's double-chocolate chip muffins as our secret weapon against DS' tendency to sleep in; all we have to do is offer him one and he's out of bed like a shot.