those two option are essientially the same, the HD6990 is 2 x HD6970 cores and as long as you flick the BIOS switch to HD6970 clocks you'll have the same performance as 2 x HD6970's.
2 x HD6970's would take up 4 slots and 2 x PCIE lanes, the HD6990 would only take up 2 slots and 1 x PCIE lane.
Both solutions will be noisy, no doubt about that, I'd go for the cheapest option.