With $1k you have plenty of options for GPUs. However if you are not already water cooling the cost to get running will eat into your budget. If you buy an EK 360 kit you are looking at around $300 plus at least $120 per GPU block. So let's say you do go water with a GPU block $450 with shipping cost is gone. That leaves $550 for a GPU. 290x or 780 are your choices. Both can play games on ultra. Sli or Xfire is out of the question be you will need another block and have to get a thicker rad or add another rad to cool 2 top GPUs and a OC i5.
If you skip Water and just use an AIO on CPU, 2x 770s or 2x 290s might be the way to go.