If this is going to be a final purchase I would likely side with the 6970's.
If there is any remote possibility of later crosfiring 2 6990's I would definitely go with them.
The primary difference I think here would mainly be future expansion, which would still be possible with the 6990 but not so much when you already have 2 6970's.
The performance will be relatively equal from what little I could find comparing the two scenarios online.
As always the single card will likely cause less heat in the case. It's the reason I've quit doing sli/crossfire myself.
The heat produced by two cards working overtime in such a tight space just never jived for me.
Despite really good airflow I was forced to take the side off my case and use a house fan when I was pushing sli in the past myself.
Otherwise the cards hovered dangerously close to shut off temps under stress.