Begin by making the cream cheese filling. Line a plate or cutting board that will fit in the freezer with parchment paper. Set aside.
In the bowl of a stand mixer, combine the softened cream cheese, sugar and vanilla. Cream for about 2 minutes or until smooth and fluffy looking. Transfer the filling to a piping bag and cut a small hole in the end. Pipe 42 small mounds about the size of a quarter. We will be using three for each cookie. Transfer the sheet to the freezer while you continue making the cookie dough. They should be set up by the time you need them.
To make the sugar coating: In a small bowl combine the sugar and pumpkin pie spice. Whisk to combine and set aside.
Preheat the oven to 350 degrees. Line two cookie sheets with parchment and set aside.
In the bowl of a stand mixer, combine the softened butter and brown sugar. Cream for about 2 minutes.
Add in the egg yolks and vanilla and mix again until lighter in color and smooth.
Combine with the pumpkin puree, flour, pumpkin pie spice, baking soda, baking powder and salt. Mix until thoroughly combined. Stop the mixer, scrape down the sides and mix again. Dough will be sticky.
Scoop out a heaping tablespoon worth of cookie dough (should get you about 14 portions worth). Remove the cream cheese from the freezer and place 3 rounds in the center of the dough. Enclose the cream cheese in the center of the cookie dough and roll into an even ball, making sure that the cream cheese is hidden and not peeking through the dough. Roll each cookie dough ball in the spiced sugar coating. Transfer to the cookie sheets, leaving plenty of space between to allow for spreading.
Once all cookies are shaped and on the baking sheet, sprinkle the remaining sugar mixture over the cookies for an added little crunch.
Bake in the preheated oven for 12 minutes or until edges are set and slightly browned. The center will remain soft with a slightly crunchy exterior.
Transfer to cooling rack to cool.