The correct form is "sino que son", all together. "Sino" can be translated as "but": Three buildings are not green, but black. So you can use "tres edificios no son verdes, sino negros" or "tres edificios no son verdes, son negros", it doesn't matter which. By the way, the sentence doesn't have too much sense because nobody knows which buildings are... it would be better if you say "Esos/estos/aquellos tres edificios..."