The Best GPU which you can use with MATLAB is going to be the Nvidia Tesla K80 meant for server systems. It runs around $5,000 USD. It's predecessor the K40 runs about $3,000, but the K80 is basically 2 of these in one. With that in mind I assume there may be a cost issue involved, so I will also mention the NVidia Titan Z which runs about $1500. All of these are great for double precision. If you need to further constrain this budget (or if single precision is fine for your problem) you could consider the Titan X or the GeForce 980 ($1200 and $700 respectively).