Preheat the oven to 350°F (176°C) and line muffin pans with cupcake liners or lightly grease with cooking spray. This recipe yields 14-16 cupcakes, so you'll need two pans.
In a medium bowl, whisk together the flour, baking powder, baking soda and salt.
In a large bowl, cream the butter, sour cream, sugars and pudding mix on high speed until smooth. Beat in the egg and vanilla, scraping down the sides of the bowl to ensure that ingredients are evenly incorporated.
Mix in half of the flour on low speed, until just combined. Slowly mix in the milk, followed by the remaining flour. Fold in the chocolate chips by hand.
Fill each prepared muffin cup 2/3 full. For a more even baking, fill any empty cups 2/3 full of water. Bake the cupcakes one pan at a time for 16-20 minutes, or until a toothpick inserted into the center comes out clean and the edges are lightly browned. (Be wary of the chocolate chips, which might make it a little more difficult to assess doneness.)
Let the cupcakes rest in the pan for 5 minutes before removing them to a wire cooling rack.