In a medium pot, heat the olive oil and add the onions. Season with salt and pepper. Cook over medium heat until the onions start to brown, then reduce the heat to low and cook, stirring often, until the onions are caramelized; this will take between 30 and 40 minutes.
Add the beef stock and bouillon cube and simmer until the liquid has been absorbed into the onions. Stir in the sherry vinegar and thyme and season with salt and pepper. Transfer to a medium bowl and set aside to cool completely.
Add the sour cream and cream cheese to the onion mixture and stir to combine. Place the dip in a serving bowl and top with the chives and lemon zest. Serve with the crostini.