Boil cubed potatoes in salted water until fork-tender, about 15-20 minutes. Drain well and mash until smooth.
Meanwhile, sauté diced onion in 3 tablespoons butter until golden and caramelized, about 8-10 minutes.
Mix mashed potatoes with caramelized onions, cream cheese, salt, and pepper. Let cool completely before using.
Make the Dough
In a large bowl, whisk together flour and salt. Create a well in the center.
Beat egg with sour cream, warm water, and melted butter. Pour into flour well.
Mix until a soft dough forms, adding more water if too dry or flour if too sticky. Knead briefly until smooth.
Cover and let rest for 20 minutes while filling cools.
Assemble Pierogi
Roll dough on floured surface to 1/8-inch thickness. Cut into 4-inch circles using a bowl or large cookie cutter.
Place 1 tablespoon filling in center of each circle. Brush edges with water.
Fold dough over filling and seal edges firmly with fork tines. Place on parchment-lined baking sheets.
Cook and Serve
Bring large pot of salted water to boil. Add pierogi in batches, don't overcrowd.
Cook until they float to surface, about 3-4 minutes. Remove with slotted spoon.
For extra golden finish, heat butter in large skillet and pan-fry boiled pierogi until golden on both sides.
Serve hot with caramelized onions, sour cream, and fresh chives.
Notes
Storage tip: Freeze uncooked pierogi on baking sheets, then transfer to freezer bags for up to 3 months. Cook straight from frozen, adding 1-2 extra minutes. Cooked pierogi keep in fridge for 4 days and reheat well in a skillet with butter.