Are you using these solely for mining or as a regular PC too?

I would also go with the first one, heres why:

The 6990 card alone can do the same as the 2 6970s in terms of Mhash/s (give a few tweaks here and there). Also powering one device as apposed to w will be less heat/power consumption. You also have the option of getting another 6990 later on if you want to add into it.

My only issue with both machines are they seem a tad expensive. If they are just miners then you can probably cut down on the motherboards and CPUs - ie not get such fancy ones and save some cash.