Line a 12 cup muffins tin with cupcake liners. Fill each cupcake hole with one vanilla wafer. Set aside.
In a medium bowl, cream the brown sugar, granulated sugar and butter until combined, about 3 minutes. Add the vanilla and salt and mix well. Add the flour and milk and beat until well-combined, about 2 minutes. Add another tablespoon of milk if it needs to come together better. It should be a consistency of cookie dough. Add the mini chocolate chips and stir together until incorporated.
Scoop one tablespoon of edible cookie dough and roll into a ball. Press gently into the muffin tins on top of each vanilla wafer. Set aside.
Add the cream cheese to a medium bowl and beat until whipped, about 3 minutes. Add the pudding mix and milk and beat until combined. Mixture should be smooth.
Scoop one tablespoon of cheesecake on top of the cookie dough layer. Refrigerate for 20 minutes. Top with whipped cream and mini chocolate chips and enjoy.