In a large skillet over medium heat, melt butter and add sliced onions. Cook for 15-20 minutes, stirring occasionally, until onions are golden brown and caramelized. Add balsamic vinegar during the last minute of cooking. Set aside to cool slightly.
In a large bowl, mix together cream cheese, sour cream, and mayonnaise until smooth and well combined.
Stir in 1½ cups Gruyere cheese, mozzarella cheese, garlic powder, thyme, salt, and pepper.
Fold in the caramelized onions and three-quarters of the crumbled bacon, reserving some bacon for topping.
Transfer the mixture to a slow cooker and smooth the top. Sprinkle with remaining ½ cup Gruyere cheese.
Cover and cook on LOW for 2 hours, or until the dip is hot and bubbly around the edges.
Top with reserved bacon crumbles and fresh chives. Serve warm with crackers, bread cubes, or veggie sticks.