Line a baking sheet with parchment paper. Set aside.
In a small bowl, whisk together flour, baking soda and salt. Set aside.
In the bowl of a stand mixer, beat together butter, brown sugar, granulated sugar, milk and vanilla until combined.
Fold in the flour mixture and chocolate chips.
Refrigerate for 15 minutes then scoop out 2 tablespoons dough and shape into a ball. Place on prepared baking sheet. Freeze at least 4 hours or overnight.
Preheat oven to 350°F. Line two cupcake tins with paper liners. Set aside.
In a large bowl, whisk together flours and set aside.
In the bowl of a stand mixer fitted with a paddle attachment, add butter. Beat until light and fluffy. Add sugar slowly in 3 additions. Add eggs one at a time, beating after each addition and scraping down sides as necessary.
Add flour, alternating with milk and mixing just until combined after each addition. Add vanilla and mix once more.
Divide batter evenly among prepared cupcake tins. Place one ball of frozen cookie dough on top of each cupcake. Bake in preheated oven for 20 minutes. Remove cupcakes from oven and cool completely on a wire rack.
In the bowl of a stand mixer fitted with a whisk attachment, beat confectioners’ sugar and butter on low speed until combine, about 1 minute.
Increase speed to medium and continue beating 3-4 more minutes.
Add vanilla and heavy cream. Beat 2 more minutes.
Frost cooled cupcakes then garnish with a miniature chocolate chip cookie.