In a large mixing bowl, beat cream cheese until smooth.
Add sugar and vanilla, beating until smooth.
Add eggs, one at a time, beating well and scraping the bowl after each addition. Do not add eggs all at once, and then beat. Add one-by-one, beating well after each. It's best if eggs are at room temperature because they incorporate easily and prevent overmixing, but it's not absolutely necessary.
Beat in spices and pumpkin puree until combined.
Pour pumpkin cheesecake batter over crust.
Evenly distribute the chilled cookie dough balls over the pumpkin cheesecake batter. Once on top of the batter, push them down, making sure they are entirely covered by batter. They do not have to be pushed down to the bottom of the cheesecake, only enough that they are covered by batter. No edges of cookie dough balls should be exposed.
Bake at 350 degrees for about 75 minutes, or until edges are golden, and center appears set. It will be slightly jiggly when lightly shaken (it will fully set as it cools), but most importantly, it should not seem liquidy, especially toward the center.
Remove to a wire rack to cool completely.
Run a knife around the edges of the cheesecake to loosen, release the edges of the springform pan, and remove. Leave the cheesecake still sitting on the bottom part of the springform pan -- we'll transfer the cheesecake later.
Refrigerate cheesecake until thoroughly chilled.
Transfer to a serving platter, removing the bottom of the pan carefully.
Prepare ganache and garnish.