Preheat the oven to 350 degrees F (175 degrees C). Line a 9x13-inch baking dish with aluminum foil and lightly grease with cooking spray.
Combine graham cracker crumbs, melted butter, and 2 tablespoons sugar in a bowl. Mix until butter evenly coats the crumbs. Transfer to the baking dish and flatten into an even layer.
Bake in the preheated oven until lightly browned, 8 to 10 minutes. Leave oven on; remove crust and let cool.
Place cranberries, water, and 1/4 cup sugar in a saucepan over medium-high heat. Bring to a boil. Cook until cranberries have burst and mixture is thick, about 7 minutes. Let cool for 15 minutes. Pour sauce into a blender or food processor and puree until smooth, adding more water to thin, if necessary.
Combine remaining sugar and cream cheese in a bowl. Beat using an electric mixer until smooth, scraping down sides of the bowl every 90 seconds, about 4 minutes total. Add eggs 1 at a time, beating well after each addition. Add milk, lemon juice, and almond extract; mix batter on medium-low until combined.
Spread batter evenly over the cooled crust. Drop spoonfuls of cranberry sauce on top and use a knife to swirl it through the batter. Toss almonds evenly over the cheesecake.
Bake in the preheated oven until set, 27 to 33 minutes. Let cool, at least 30 minutes. Refrigerate until set, 8 hours to overnight. Cut into bars the next day.