They both have their strong points, however if it's crossfire 7970's vs a single 690 then the obvious choice is the 7970's. And the driver problems are over exaggerated, since catalyst controller, the driver issues are very rare.
One big problem with Crossfire is that it does not meter out frames evenly. Of course, we have all heard about the microstutter issue, but what has been coming to light over the past several months is that the frame metering problem leads to an issue where traditional methods of measuring FPS (Hardware FPS below) are actually inflating the scores for Crossfire (Practical FPS below).
In a nutshell, the performance of Crossfire, when measured accurately, is often no better than the performance of a single card and then is often even worse than a single due to frame latency and microstuttering. SLI is not affected by this problem. This has been documented and discussed in nearly every major review site and fully admitted by AMD. They are currently working on a "Prototype" driver to address the issue (also in the chart below). The GTX 690 is a clear winner here.
I have Sapphire 7970 ghz crossfire and i absolutely love it. Sure there is micro-shutter but i think that is blown out of proportion because i barely notice it and i am on the 13.6 beta drivers. I run a 5760x1080 setup