In a big bowl, beat together the cream cheese and peanut butter, until smooth, scraping down the sides of the bowl as needed. Add the sugar and flour, and beat on medium speed until combined. Add the eggs, one at a time, beating on low speed after each addition until just combined. Beat in the vanilla extract. Divide cheesecake mixture among cupcake cups filling each cup nearly full. Bake for 20-23 minutes. Don't over bake. It should be slightly jiggly in the middle. Remove from oven and allow to cool completely at room temperature, at least 1 hour, before adding chocolate ganache.