Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
Make the streusel: In a small bowl, mix flour, brown sugar, and cinnamon.
Cut in the cold butter with a fork until crumbly. Chill while you make the batter.
Whisk dry ingredients: In a medium bowl, whisk flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
Cream butter and sugar: In a large bowl, beat butter and granulated sugar until light and fluffy, about 2–3 minutes.
Add eggs and vanilla: Beat in eggs one at a time, then add vanilla. Scrape the bowl as needed.
Combine wet ingredients: Stir milk and yogurt together in a small measuring cup.
Finish the batter: Add half the dry mix to the butter mixture, then half the milk-yogurt.
Repeat, mixing just until combined. Do not overmix.
Fold in berries: Toss blueberries with 1 tsp flour, then gently fold into the batter.
Fill the liners: Divide batter evenly among the cups, about 3/4 full. Sprinkle each with a little streusel.
Bake: Bake 18–22 minutes, until tops are set and a toothpick comes out with a few moist crumbs.
Cool in pan 5 minutes, then move to a rack to cool completely.
Make the frosting: Beat cream cheese and butter until smooth. Add powdered sugar gradually, then maple syrup, vanilla, and a pinch of salt. Adjust thickness with more sugar or a drizzle of maple.
Frost: Once cupcakes are fully cool, pipe or spread frosting.
Finish with a tiny drizzle of maple syrup or a pinch of cinnamon, if you like.