I have built dozens of GPU rigs to date, and the setup that gives you best mining yield for dollar requires 3 or 4 GPUs, currently the R9 280x. This will, however, cost your around $1800 to build.

What you can do, is create an excel file with all part's list and cost with automated calculation (I did that before), and it will be very clear what optimum setup you can get for $1000.