Preheat the oven to 325°F (163°C). Line an 8x8-inch baking pan with parchment paper.
In a bowl, mix graham cracker crumbs, 3 tablespoons sugar, and melted butter until combined. Press the mixture firmly into the bottom of the pan.
Bake the crust for 8 minutes, then let it cool slightly.
In a large mixing bowl, beat cream cheese and 1/2 cup sugar until smooth and creamy.
Add eggs one at a time, beating well after each addition.
Mix in lemon juice, lemon zest, and vanilla extract.
Toss blueberries with flour to coat them lightly, then fold them into the batter.
Pour the cheesecake mixture over the cooled crust and smooth the top.
Bake for 35-40 minutes, or until the center is set.
Cool to room temperature, then refrigerate at least 3 hours before slicing.