What is the best way to thaw these muffins once frozen?

I've made and frozen these a few times. I often just put them in the oven to toast straight from frozen. After they thaw enough to split, I split them and finish toasting the two halves. If I am at home for a while before I know I'll want them, sometimes I thaw them by leaving them out on the counter for a while (wrapped in saran wrap) or in the fridge for a longer period of time. But in general I think it's best to just toast from frozen (unless you are trying to avoid toasting the muffin at all - but they're great toasted!)
I too freeze them very tightly wrapped in saran wrap, then in a freezer bag.

I freeze baked goods very tightly wrapped, individually, in plastic, then consolidated in large freezer bags. Then I just take however many I need out, and allow to thaw completely (still wrapped), on the counter. If you unwrap them before they're thawed, moisture will condense on the surface and make the baked good soggy. This may not be the fastest way to thaw, but its the most successful.

I adore these muffins and make them all the time. I find that microwaving on high for about 20 seconds is a good start. If they still feel cool, I slice them in half and microwave for another 20 seconds. These freeze beautifully.