In a saucepan over medium heat, combine blueberries, sugar, and lemon juice; cook until berries soften and juices release, mashing frequently.
Whisk water and cornstarch together, then add to the saucepan; cook 1-2 more minutes until sauce thickens, then remove from heat.
Strain the sauce through a fine-mesh strainer into a bowl, discarding solids; set blueberry sauce aside to cool.
Preheat oven to 325°F; line muffin pans with cupcake liners.
Mix graham cracker crumbs, sugar, and melted butter until combined; distribute evenly in the muffin liners, pressing firmly.
Bake crusts for 5 minutes; remove and allow to cool while maintaining oven temperature.
Beat cream cheese and sugar in a mixer until smooth; add lemon juice, zest, and vanilla; mix to combine, scraping sides as needed.
Add eggs one at a time, mixing on low speed just until combined after each addition.
Fill muffin liners evenly with cheesecake batter.
Top each cheesecake with about 1 teaspoon of blueberry sauce and gently swirl with a toothpick.
Bake cheesecakes at 325°F for 17-20 minutes until set but slightly wobbly in the center.
Cool cheesecakes at room temperature for at least 1 hour, then refrigerate in an airtight container for 3-4 hours or overnight before serving.