Preheat the oven to 350°F and line a 12-cup muffin pan with paper liners.
Whisk the flour, baking soda, baking powder, and salt together in a medium bowl.
In a large bowl, whisk the mashed bananas, granulated sugar, and brown sugar. Beat in the egg, oil, and 2 teaspoons vanilla, then slowly whisk in the dry ingredients until no lumps remain. Fold in the pecans and fill the liners three-quarters full.
Beat the softened cream cheese until smooth. Add the topping sugar, egg yolk, and 1 teaspoon vanilla and beat until combined. If needed, beat in the milk to loosen it.
Top each muffin with about 1 tablespoon of the cream cheese mixture and swirl it into the batter with a toothpick.
Bake for 16 to 18 minutes, until a toothpick inserted into the center comes out clean.
Serve fresh. Store leftovers in an airtight container in the refrigerator and bring them to room temperature or serve slightly chilled.