I would go with CUDA.
I work in image processing and have been trying hardware add-ons for years. First we had i860, then Transputer, then DSP, then the FPGA and direct-compiliation-to-hardware.
What innevitably happened was that by the time the hardware boards were really debugged and reliable and the code had been ported to them - regular CPUs had advanced to beat them, or the hosting machine architecture changed and we couldn't use the old boards, or the makers of the board went bust.
By sticking to something like CUDA you aren't tied to one small specialist maker of FPGA boards. The performence of GPUs is improving faster then CPUs and is funded by the gamers. It's a mainstream technology and so will probably merge with multi-core CPUs in the future and so protect your investment.
