Given the fact that AMD cards typically have lower power consumption than their Nvidia counterparts, I would have to guess that the 6990 is going to be faster than the 590 at stock speeds. With dual GPU cards, the limiting factor is the 300w ceiling dictated by PCI-SIG. And since AMD seems to be able to get more performance per watt than Nvidia, the 6990 should be the faster of the two cards.Looks like Nv will have the fastest dual GPU as well. Although price, power consumption will likely weigh heavily on that privilege.
Of course, once you start overvolting/overclocking it's anybody's guess as to which one will come out on top.