As an owner of both, I say go for the rear rack. My roof rack on my small/medium SUV (Jeep Liberty) is hard to reach with cycling shoes on. My wife also tried to drive the vehicle inside the garage once - I ended up buying a new comunter bike from that mishap.

People used to say roof racks keep bikes safer in the event of a rear end colision. That sounds good but if you get a rear end accident, you probably have more things to worry about than your bike.

Roof racks also cause wind noise so get the air deflector. They cost much more. They keep you from being able to use many automated car washes. They also make it difficult to wash parts of the car by hand.