Preheat oven to 350 degrees. Make the cupcakes: Sift together flour, baking powder, and 1/4 teaspoon salt. Stir together milk and vanilla.
Beat butter and sugar with a mixer on medium speed until pale and fluffy, about 3 minutes. With mixer running, add eggs, 1 at a time. Beat in flour mixture in 3 additions, alternating twice with milk mixture.
Line a standard muffin tin with baking cups. Fill each with 1 tablespoon batter, 1 heaping tablespoon chopped nectarines, and an additional 2 tablespoons batter. Bake until edges begin to turn golden, about 25 minutes. Let cool in tin.
Make the topping: Whisk together cream, sour cream, and sugar to medium peaks. Top cupcakes with a dollop of cream and nectarine slices.
Peaches, plums, or apricots work just as well as nectarines.