Preheat oven to 375 degrees. Generously butter or grease a standard 12-cup muffin pan and dust with flour, tapping out excess; set aside. In a medium bowl, whisk together flour, baking powder, and salt. In another bowl, toss cranberries with about 1 1/2 teaspoons flour mixture to lightly coat; set aside the flour mixture and the cranberries.
In the bowl of an electric mixer fitted with the paddle attachment, or using a handheld mixer, beat butter and sugar on medium-high speed until light and fluffy, about 3 minutes. Add the 2 eggs, one at a time, beating until combined. Add cinnamon, cloves, and nutmeg.
With the mixer on low speed, add reserved flour mixture, beating until just combined. Add milk and vanilla, beating until just combined. Do not overmix. Using a rubber spatula, fold in the cranberries. Divide batter evenly among the prepared muffin cups.
If desired, in a small bowl, mix together about a tablespoon of sugar and cinnamon. Sprinkle sugar mixture on top of muffin batter.
Bake, rotating pan halfway though, until muffins are golden brown and a cake tester inserted in the center of one muffin comes out clean, about 25-30 minutes. Transfer pan to a wire rack to cool 10 minutes. Serve warm or at room temperature.