Preheat oven to 350 degrees F (175 degrees C). Line a muffin tin with paper liners.

Whisk flour, baking soda, baking powder, and salt together in a bowl.

Combine white sugar, brown sugar, and 1/4 cup butter in another bowl; beat with an electric mixer until creamy. Beat in egg. Mix in mashed bananas. Add flour mixture in 3 batches, alternating with buttermilk, stirring after each addition. Fold chocolate chips into the batter.

Spoon batter into the prepared muffin tin.

Bake in the preheated oven until a toothpick inserted in the center comes out clean, about 20 minutes. Cool cupcakes on a wire rack, about 30 minutes.

Beat cream cheese and 3 tablespoons butter in a bowl until smooth. Add vanilla extract. Beat in confectioners' sugar, 1 cup at a time, until frosting is smooth.

Spread frosting over cupcakes.