Preheat your oven to 325°F (163°C) and line a muffin tin with paper liners.
In a small saucepan over medium heat, combine the crushed pineapple, brown sugar, butter, and 1/2 teaspoon vanilla extract. Cook for about 5 minutes, stirring occasionally, until the mixture is slightly thickened. Remove from heat and set aside.
In a mixing bowl, combine the graham cracker crumbs, granulated sugar, and melted butter. Stir until the mixture resembles wet sand.
Press about 1 tablespoon of the graham cracker mixture into the bottom of each muffin liner to form the crust.
In a large mixing bowl, beat the softened cream cheese until smooth. Gradually add the powdered sugar and mix until well combined.
Add the eggs one at a time, mixing well after each addition. Stir in 1 teaspoon of vanilla extract until fully incorporated.
Spoon the cream cheese mixture over the crusts in the muffin tin, filling each liner about 2/3 full.
Add a spoonful of the pineapple mixture on top of each cheesecake.
Bake in the preheated oven for 20-25 minutes, or until the edges are set and the centers are slightly jiggly.
Remove from the oven and let cool at room temperature for about 30 minutes, then refrigerate for at least 2 hours before serving.