Whisk flour, baking powder, and salt together in bowl. Using stand mixer fitted with paddle, beat cream cheese, butter, and sugar until smooth and creamy, about 2 minutes. Add eggs and vanilla an mix until incorporated. Reduce speed to low, add flour mixture, and mix until just combined. Cover bowl tightly with plastic wrap and refrigerate until firm, about 30 minutes.
Adjust oven racks to upper-middle and lower-middle positions and heat oven to 350 degrees. Line 2 baking sheets with parchment paper. Spread graham cracker crumbs in shallow dish.
Roll dough into 1 1/2-inch balls (about .9 oz each), then roll in graham cracker crumbs; space dough balls 2 inches apart on prepared sheets. Using 1-tablespoon measure, make indentation in center of each dough ball. Using a fork, pick up 3 cherries from the pie filling and let most of the liquid drip back into the bowl (less of the filling to prevent the cookies from being soggy). Place 3 cherries in each indentation.
Bake until golden around edges, 12 to 14 minutes, switching and rotating sheets halfway through baking. Let cookies cool for 5 minutes on sheets, then transfer to wire rack. Let cookies cool completely before serving.