If both are 2008-2009, then X5
I was faced with almost similar condition, but it was 2008 X5 3.0si to 2011 BMW X3 20d. I picked the X3 mainly because the size of the new X3 is just right for my needs, not too big and not too cramped, and 2.0 diesel efficiency is a big plus since I drive the car mainly in slow moving traffics. Also I think the new X3 is much more improved, it rides and drives much better than the first gen X3.
Of course all of this is just my opinion, you should go and test drive the cars yourself
