They mean about the same thing, but if you use 楼 in certain situations it can also mean e.g. your house is on the second floor.

When talking about a particular level of a building, you can use either 楼 or 层: second floor = 二楼 = 二层, although 楼 is more colloquial. When counting the number of levels/stories of a building, each level/story is called a 楼, but you have to use the classifier 层: two stories = 两层楼 (compare: two books = 两本书).