CUDA vs FPGA for Image Processing; which is better
Did you have a chance to look at Spiral site?  They try to address this question.  For example, there are special cases where FPGA will run O(N) instead of the customary O(N log N).

Here's a paper that deals with generating FPGA.

All the way at the end of benchmarks page they show performance of a software algorithm enhanced with FPGA-based solvers.

P.S.  It's worth noting that Spiral can be used to optimize algorithms other than FFT, but presented data outlines the popular case only.