Preheat oven to 400 degrees F. Lightly grease thirty-six 1-3/4-inch muffin cups or line with paper bake cups; set aside.
For topping, in a mixing bowl, beat cream cheese, granulated sugar, 1 tablespoon flour, and the egg yolk with an electric mixer on medium speed until blended. Fold in chocolate pieces; set aside.
In a bowl, stir together 1-3/4 cups flour, the brown sugar, cocoa powder, baking powder, cinnamon, salt, and baking soda. Make a well in center of flour mixture; set aside.
In another bowl, combine egg, milk, oil, and vanilla. Add egg mixture all at once to flour mixture. Stir just until moistened (batter should be lumpy). Fold in nuts.
Spoon batter into prepared muffin cups, filling each two-thirds full. Spoon cream cheese topping on top of the batter in each cup. Bake about 12 minutes or until edges spring back when lightly touched (do not touch cream cheese topping). Cool in muffin cups on a wire rack for 5 minutes. Remove from muffin cups; cool completely. Cover; store in refrigerator.