Combine the Swiss chard, onions and 1/2 cup water in a large pot. Bring to a simmer over high heat, lower the heat to medium, cover and cook, stirring frequently, until the chard is very tender, about 15 minutes.
Meanwhile, combine the cream cheese, nutmeg and 1/4 cup water in a medium saucepan. Place over medium heat and cook, whisking frequently, until the cheese melts and the mixture just bubbles around the edges. With a slotted spoon, transfer the chard to the pan with the cheese mixture (leave any excess liquid in the pot). Mix well and season with salt and pepper. Garnish with the pine nuts.