Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
In a medium bowl, beat the softened cream cheese, 1/4 cup sugar, 1 egg, and vanilla extract with an electric mixer on medium speed until the mixture is completely smooth and free of lumps. Set the cheesecake filling aside.
In a large bowl, stir together the brownie mix, vegetable oil, water, and 2 eggs until just combined and no dry streaks of mix remain. Gently fold in the chocolate chips.
Divide about two-thirds of the brownie batter evenly among the prepared muffin cups, filling each about halfway full. Spoon the cream cheese mixture evenly over the brownie batter in each cup. Top each with a dollop of the remaining brownie batter, using a spoon to gently swirl it into the cheesecake layer.
Bake for 20-25 minutes, or until the edges of the brownies are set and the tops appear dry. The centers will still be slightly soft. Allow the cups to cool completely in the muffin tin on a wire rack before serving.