Make the batter: Preheat oven to 350°F with a rack in the middle position; line 2 standard muffin tins with paper liners. In a medium bowl, whisk together flour, cinnamon, baking powder, baking soda, and salt.
In a large bowl using a hand mixer or in the bowl of a stand mixer fitted with the paddle attachment, beat butter and sugars together on medium speed until creamy. Add egg and vanilla and beat to combine. Scrape down sides of the bowl to make sure all is evenly incorporated. Add dry ingredients and beat on low speed until just a few dry streaks remain. Add milk and beat to combine. Fold in apples. Fill liners ¾ full with batter (you should get about 15).
Make the topping: In a medium bowl, combine melted butter, sugars, cinnamon, and a pinch of salt. Mix in flour until large crumbs form. Divide crumbs evenly over muffins.
Bake until a toothpick inserted in the middle of a muffin comes out clean, 20 to 22 minutes. Let cool slightly before serving.
