Preheat oven to 425°F. Line (2) 12-cup muffin pans with 6 cupcake liners in one and 7 in the other, skipping every other cup so the muffins have room to grow without touching each other. One pan will have two liners next to each other, but it should be okay when the muffins bake.
In a medium mixing bowl, whisk the flour, pumpkin pie spice, baking powder, baking soda, and salt together until well combined. Set aside.
Place the butter, sugar, and brown sugar in a separate large mixing bowl, and use an electric mixer to mix until light and fluffy.
Add the pumpkin puree and sour cream and continue mixing until combined. Then, add the eggs and vanilla extract and mix until the eggs are just incorporated.
Alternate adding the dry ingredients and the milk until both are just incorporated and the batter is smooth, then fold in the chocolate chips.
Use a cookie scoop to scoop the batter into the cupcake liners. Fill them to the top of the cup (I like to add a little bit more batter on top for very tall muffins), then add some extra chocolate chips on top.
Bake the muffins, one batch at a time, for 7 minutes, then reduce the temperature to 350°F (do not open the oven). Bake for another 13-15 minutes or until a toothpick inserted into the center of the muffins comes out clean.
Let the muffins cool in the pan for 10 minutes before transferring them to a cooling rack to cool completely. Store in an airtight container for up to 3 days.