South-facing window is the best passive solar option. Skylight may allow too much sun in the summer.
During the winter, we open the shades on the south and east facing window for the solar gain we can get. It helps that we ahve a darker tile in the diningroom, that soaks up alot of heat during the day. Some days there is enough sun-heat that the furnace never kicks in until early evening (when the sun is setting).
I am wondering if you put a row of concrete block inside, infront of the window to soak up the sunlight it would help to add warmth to the coop?
In my growhouse, I have a row of plastic bottles that I spray painted black, filled with water, then patially burried in a pea gravel. Even with 9 degrees the other night, and every night for the past 1 1/2 weeks below freezing, I still have spinach growing in there. And it is only covered in plastic!