Preheat oven to 350°F. Spray 2 regular sized muffin tins with cooking spray.
Whisk together flour, baking soda, and salt, set aside.
Beat butter and sugars on med-high until light and fluffy (approx. 2-3mins). Reduce speed and add eggs (one at a time), and vanilla. Beat until combined.
Add flour mixture a little at a time and mix until just combined.
Using a large cookie scoop (3 Tbsp) scoop dough into muffin tins, press down to flatten slightly.
Bake for approx. 15mins or until browned and mostly set.
Remove from oven and immediately use a small jar or container to press firmly down in the center to create a well. Cool in pans for 15mins, then place on wire rack to cool completely.
Place sugar and water into a medium pot, stir to combine, but to not stir from this point forward. Cook over high heat, washing down the sides of the pot with a pastry brush dipped in water as needed to prevent crystals.
Cook until desired color of caramel is reached and immediately remove from heat. Very slowly, add heavy cream. The mixture will bubble up (a lot) and boil. Add butter, return to heat, and bring back to a boil. Cook for 2 minutes stirring constantly.
Remove from heat and let cool to room temperature. Transfer to a container and place in fridge to thicken.*
Place chopped chocolate and cream into a microwave safe bowl. Stir to combine. Microwave for 20 seconds, stir. Microwave in 10 second intervals, stirring in between, until smooth and silky. Set aside to cool completely before using.**
Using a measuring cup or a teaspoon, pour some of the thickened caramel into each cup. Place in freezer for 30mins to set.
Remove from freezer and use the same method to top with ganache. Sprinkle with sea salt if desired and place in fridge to set.
* I let mine sit in the fridge overnight. ** The ganache can sit on the counter overnight. Place plastic wrap directly onto ganache to prevent a skin from forming.