Place muffin cup liners in 12 muffin cups; coat with cooking spray.
Weigh or lightly spoon 6.75 ounces (about 1 1/2 cups) flour into dry measuring cups; level with a knife. Combine 6.75 ounces flour, baking powder, salt, and baking soda in a small bowl, stirring with a whisk. Combine granulated sugar, cream cheese, and 1/4 cup butter in a large bowl; beat with a mixer at high speed until well blended. Add amaretto, vanilla, and egg to sugar mixture; beat with a mixer at medium speed until well blended. Combine sour cream and 1/4 cup milk in a small bowl; stir with a whisk until well blended. Combine apple and 1 tablespoon flour in a small bowl; toss well.
Add flour mixture and sour cream mixture alternately to sugar mixture, beginning and ending with flour mixture. Beat just until blended. Fold in apple mixture. Divide batter evenly among muffin cups.
To prepare the streusel, combine 2 tablespoons flour, brown sugar, and ground cinnamon in a small bowl. Cut in 2 tablespoons butter with a pastry blender or 2 knives until mixture resembles coarse meal; stir in almonds. Sprinkle streusel evenly over cupcakes. Bake at 350° for 27 minutes or until a wooden pick inserted in center comes out clean. Cool in pan for 15 minutes on a wire rack, and remove the cupcakes from pan.
To prepare glaze, combine powdered sugar and 4 teaspoons milk in a small bowl, stirring with a whisk. Drizzle glaze over cupcakes.