Preheat the oven to 375 degrees and place 12 paper liners into each well of your standard size muffin baking pan.
In medium bowl, whisk together flour, sugars, baking soda, salt and spices until evenly combined. Set aside.
In another bowl, whisk together the eggs, pumpkin puree, coconut oil and vanilla extract. Make sure coconut oil is slightly cooled after melting so that the eggs don't cook.
Pour the wet ingredients into the dry ingredients and fold with a rubber spatula. Do not over mix, just stir until everything is incorporated into the batter. Gently fold in chocolate chips just until evenly distributed. The batter will be thick. That is okay.
Evenly distribute batter between prepared muffins cups. I use a cookie scooper to minimize the mess. You want to muffins to be almost full as the muffin will bake up in the oven.
Bake your muffins for 20-22 minutes or until a toothpick inserted into the center of a muffin comes out clean. Set aside to cool.
(Optional) While muffins are cooling, make the glaze: in a small saucepan, melt the butter over medium-low heat and continue to cook, swirling occasionally, until butter foams first, and then turns golden brown and has a nutty aroma.
Immediately after browning, pour butter into a medium bowl. To the browned butter, add the powdered sugar, vanilla, and 3 tablespoons of milk. If the glaze is too thick, add an additional tablespoon of milk.