In a food processor or mini-chopper, pulse the gingersnaps until finely ground. In a medium bowl, add the gingersnap crumbs, brown sugar, ginger and melted butter; stir until well combined.
Lightly butter or grease a 9” springform pan. Line the bottom of the pan with a circle of parchment paper. Press the crust mixture evenly into the bottom of the pan. (Tip: A flat-bottomed glass helps pack the crust mixture down evenly.)
Bake crust for 10 minutes; remove from oven and let cool.
Reduce oven temperature to 325°F.
For the Cheesecake
Using an electric mixer, beat the cream cheese on medium speed until completely smooth (~3 minutes).
Add the sugar and flour; mix until well combined.
Using a small bowl, add eggs and egg yolks; whisk until well combined. Add eggs to the bowl with the cream cheese in 2 additions, mixing fully after each addition.
Add the sour cream and vanilla; mix until well combined. (Tip: Use a spatula to scrape the sides and bottom of the bowl to ensure the filling is fully mixed.)
Remove 2 cups of batter and combine with the molasses, ginger, cinnamon, nutmeg and cloves.
Pour vanilla batter into the cooled crust. Pour gingerbread batter on top. Using a table knife, gently swirl the pumpkin batter into the vanilla batter.
Wrap the bottom of the pan with a piece of aluminum foil and place in a large baking pan. Fill pan with about ½”-¾” of water. Bake at 325°F until center of cake is just barely set (about 80-90 minutes). (Tip: Pull the cheesecake out of the oven when there is about 1" ring of "looser" filling left in the center of the cake.)
Remove cake from oven and cool for 10 min. Wrap entire pan in plastic wrap and freeze overnight.
The next day, remove the cake from the freezer and release the springform pan. Transfer the cake to a serving platter and defrost in a refrigerator for 4-5 hours.
For the Vanilla Bean Whipped Cream
Combine all ingredients in small bowl. Using a hand mixer, beat until stiff peaks form.
Using an offset spatula, spread a thin layer of whipped cream across top of cheesecake before serving.