Place chocolate chips in a bowl then pour the hot coffee over them. Mix a bit then microwave in a few 20 second intervals as needed, stirring in between. Once almost all of the chocolate is melted cover and set aside.
Add cream cheese to stand mixer fitted with a paddle attachment and mix at medium speed to cream.
Add the sugar and the salt to the bowl and mix on medium until creamy. Scrape down the bowl and mix well.
Add sour cream and vanilla extract, mix well.
Add the eggs one at a time, allowing each to incorporate before adding the next. Sprinkle in the flour and continue to mix. Scrape the bowl down and mix until smooth.
Pour in the melted chocolate and mix on low until combined. Scrape the bowl down and mix.
Pour about a cookie scoop full of the batter into the prepared cupcake wells. It's ok to fill to the top.
Bake at 325F for about 20 minutes until center is slightly jiggly. Allow to cool in muffin tin, then refrigerate at least 2 hours before topping with chocolate ganache.