Preheat the oven to 350 degrees Fahrenheit. Line two muffin tins with 14-16 paper liners.
Pulse the graham crackers in a blender or food processor until you have a fine crumb.
Add the sugar and melted butter to the graham cracker crumbs and mix them together till you have a sandy texture.
Scoop about 1 TBS of the graham cracker crumb mixture into about 14-16 different prepared cupcake liners. Press the crust down into the bottom. (You don't want it going up the sides more because then you'll have more cheesecake that you can't see in the nice layers.
Bake the crust in the preheated oven for 6 minutes.
Allow the crust to cool for a few minutes when done.
In a large bowl mix together your cream cheese, sugar, heavy cream and sour cream for about 2 minutes until combined. (Make sure to scrape the bottom and sides of the bowl)
Add in the vanilla and stir in.
Add in the eggs, and mix slowly until just combined.
Toss in your flour and salt and stir till just combined.
Separate the cream cheese mixture evenly into 3 separate bowls.
Stir in blue food coloring to one, red to one, and leave one white.
Layer a tablespoon of white cheesecake mixture into the bottom of each cup. Then a tablespoon of red, then a tablespoon of blue. Filling them each evenly about to the top.
Place the cheesecakes in the oven and bake for about 18-20 minutes. The cheesecake will still be slightly jiggly in the middle.
Remove the pans to the counter, and let the cheesecakes cool on the counter for 1 hour. Then place them in the fridge to cool completely.