I would say that the 560 Ti SLI configuration would still be better. The specs on the 2 cards (660 Ti vs 560 Ti) are very close to one another, so having the second card would provide more of an upgrade. Where the 660 Ti would have to do all of the work itself, having 2 560 Ti's would allow one card to focus on the graphics while the second handles the physics. SLI all the way.
That said, make sure your motherboard supports SLI, and that you have enough power to run your system and 2 GPUs.