Whisk together the flour, baking soda, and sea salt; set aside.
Beat the butter, white sugar, and brown sugar with an electric mixer in a large bowl until smooth. Add 1 egg and the vanilla extract and beat until smooth.
Mix in the flour mixture until just incorporated. Fold in the chocolate chips; mixing just enough to evenly combine.
Form the dough into tablespoon-sized balls; place onto a baking sheet, and freeze until solid, about 2 hours.
Beat 3 eggs in a large bowl with an electric mixer to break up.
Add the cake mix, water, and canola oil; continue beating for 2 minutes on medium speed.
Spoon into the prepared cupcake liners, filling each 2/3 full.
Place a frozen cookie dough ball on the top center of each cupcake.