Preheat oven to 425°F. Line a 12 count muffin pan with liners and spray them nonstick cooking spray and set aside.
In a large bowl, whisk the eggs, brown sugar, granulated sugar, pumpkin puree, melted butter and vanilla until combined. Add the gluten free flower, baking powder, baking soda, salt and pumpkin pie spice to the wet ingredients and gently whisk until just combined, being careful not to overmix. Add the chocolate chips, reserving a few for the tops of the muffins, and fold in gently. The batter will be thick.
Fill the muffin cups all the way full and almost overflowing. Add the reserved chocolate chips to the top of the unbaked muffins.
Bake the muffins 5 minutes at 425°F then, keeping the muffins in the oven, reduce the oven temperature to 350°F. Bake for an additional 15-18 minutes or until a toothpick inserted in the center comes out clean.
Remove the muffins from the oven and allow to cool in the pan for 5-10 minutes then transfer to a wire cooling rack to cool completely.
Store muffins in an air tight container at room temperature for up to 5 days or in the freezer for up to 3 months.