Preheat the oven to 350° and line two baking sheets with parchment paper. Set aside.
In a medium bowl beat together the cream cheese, powdered sugar, and vanilla on medium speed until smooth. Be sure the scrape down the bowl to make sure it is all well combined. Transfer to a smaller bowl and reserve in the refrigerator while you make your cookie dough.
In a large bowl, cream together the butter, brown sugar, and granulated sugar for 1-2 minutes. Add the eggs and vanilla and beat until fluffy.
Add the flour, baking soda, baking powder and salt just until combined. Add the chocolate chips and mix in by hand.
Using a medium sized cookie scoop, which is just about 2 tablespoons, scoop the cookie dough onto the baking sheets and flatten out.
Scoop about 1 ½-2 teaspoons of the cheesecake filling in the center of the flattened cookie dough and form the cookie dough up around the filling. Make sure to pinch the edges so the dough seals the filling inside.
Place the stuffed cookie balls on the baking sheet leaving 2 inches between them. Bake for 11-13 minutes, until the edges of the cookies are set and the center is still soft. The cookies will still be light in color, they won’t brown very much. Remove from the oven and let cool for 2-3 minutes on the baking sheet before transferring them to a cooling rack.