I have a Thule carrier that is great. I can mount it to my roof in under 5 minutes. I am always nervous that I am going to pull into my garage with it mounted, but haven't done it yet. I use it on my van. I have been thinking about getting a basket type instead for the 4runner. The baja racks seem like a good price point and, because they replace the factory rails, they don't really add a lot of height to the vehicle.
By the way, the Thule probably robs me of 2mpg; but completely worth it when you are traveling with kids and animals and need extra room.