Adjust oven rack to lower-middle position and preheat to 350 degrees F. Line muffin pan with baking cup liners.
In a medium bowl, sift together both flours, baking powder, salt, and 1 tablespoon cinnamon.
In the bowl of a stand mixer fitted with the paddle attachment, cream butter and sugar on medium-high speed until pale and fluffy, about 3 minutes.Beat in eggs, one at a time, until each is incorporated, scraping down sides of bowl as needed. Beat in vanilla. Reduce speed to low. Add flour mixture in three batches, alternating with two additions of milk, and beating until combined after each.
Fill the cupcake papers three-quarters full, making sure that the batter is divided evenly. Bake cupcakes until a toothpick inserted in the center of them comes out clean, about 20 minutes. Let cupcakes cool on a wire rack 10 minutes, then transfer cupcakes to a wire rack to cool completely.
In a small bowl, combine remaining 1/2 teaspoon cinnamon and 2 tablespoons sugar. Pipe cinnamon cream cheese frosting on cupcake. Dust peaks of frosting with cinnamon-sugar and top with a snickerdoodle cookie.