In a large bowl, using a high speed mixer, mix cream cheese with sugar until smooth. Stop and scrape the sides and bottom of the bowl once during the process.
Blend in milk, mix in the eggs one at a time, mixing just enough to incorporate.
Mix in sour cream, vanilla extract and flour until smooth. Stop and scrape the sides and bottom of the bowl once.
Divide the cheesecake filling evenly between 6 bowls, I used soup bowls.
Stir in the gel food colors into each one, add a few drops, stir using a spatula and if needed add more. Stir until well combined.
Add the colored cheesecake batter to the muffin cups, about 3 - 4 tablespoons per muffin cup. Add the colored cheesecake batter in the following order: purple, blue, green, and yellow, orange, red. Make sure you divide it evenly and have enough of each color for all the muffin cups.
Bake for 15-20 minutes or until the center of the cheesecake is only slightly jiggly.
Allow the cheesecakes to cool to room temperature before topping with whipped cream.