Process graham crackers in a food processor to make crumbs; pulse 1 teaspoon sugar, ginger, 1/4 teaspoon nutmeg, and 1/4 teaspoon cinnamon with crumbs once or twice to combine. With processor running, drizzle butter into crumbs just to incorporate. Press graham cracker mixture into the bottom of a 9-inch spring form pan.
Bake crust in the preheated oven for 10 minutes; cool on wire rack.
Beat cream cheese in a large bowl with an electric mixer on medium speed until smooth. Stir 3/4 cup sugar, flour, 1/4 teaspoon nutmeg, 1/4 teaspoon cinnamon, and cloves in a bowl. Beat sugar mixture into cream cheese until smooth; beat in egg. Slowly beat eggnog into cream cheese mixture, followed by vanilla extract. Pour cream cheese filling into spring form pan over the crust. Tap pan lightly on a work surface to release air bubbles.
Bake in the oven for 1 hour.
Spread sour cream over filling. Return to oven and bake 5 more minutes.
Cool in pan on a rack until cool to the touch, about 30 minutes, before refrigerating to chill thoroughly. Sprinkle with ground nutmeg to taste before serving.