Preheat the oven to 350°F. Line a standard muffin pan with paper liners.
Make the crust (10 min): Combine the graham cracker crumbs, sugar, and butter in a bowl until until it resembles wet sand. Spoon a Tablespoon of the mixture into the prepared muffin tins and firmly press down. Bake in the preheated oven for 6 minutes.
1 cup crushed graham cracker crumbs, 2 Tablespoons granulated sugar, 4 Tablespoons unsalted butter
Make the crumb topping (5 min): Using the same bowl, combine the crumb topping ingredients and use the back of a fork or pastry cutter to cut the cold butter until coarse crumbs form. Keep chilled until ready to use.
1/3 cup light brown sugar, 1/3 cup all-purpose flour, 1/4 cup quick cooking rolled oats, 1 teaspoon ground cinnamon, 4 Tablespoons unsalted butter
Make the apple filling (5 min): Stir together diced apples, sugars, flour, lemon juice, cinnamon, nutmeg, and vanilla until evenly coated. The mixture should look glossy and just starting to release juices.
2 medium apples, 2 Tablespoons granulated sugar, 1 Tablespoon light brown sugar, 1 Tablespoon flour, 1 teaspoon lemon juice, 1/2 teaspoon cinnamon, 1/8 teaspoon nutmeg, 1/4 teaspoon vanilla extract
Make the cheesecake filling (5 min): Using a handheld mixer or stand mixer fitted with the paddle attachment, beat the cream cheese and sugar on high for 2 minutes until smooth. Mix in sour cream, cornstarch, vanilla, and salt until creamy. Add eggs one at a time on low speed until just combined. Don’t over mix.
2 (8-oz) blocks full-fat cream cheese, 1/2 cup granulated sugar, 1/3 cup sour cream, 1 Tablespoon corn starch, 1 teaspoon vanilla extract, 1/4 teaspoon kosher salt, 2 large eggs
Assemble and bake (22 min): Divide cheesecake filling among liners, filling ¾ full. Divide apple filling evenly on top, then sprinkle with the crumble. Gently press it down so it adheres. Place a roasting pan or casserole dish with hot water on the lower oven rack (a water bath for humidity). Bake 20 minutes, or until centers are mostly set and edges look dry
Cool and chill (2 1/2 hrs): Cool on the counter for 30 minutes, then refrigerate at least 2 hours (or overnight) to fully set before removing liners. Top and serve chilled.