Joe -
I would think PCIe. PCIe will also be supported on more external devices than Serial RapidIO (I would think). Will you be running linux, another OS, or bare metal? Driver support is a major consideration, especially with linux. The easiest path is usually to find a reference design that runs on your target platform and copy it as closely as possible. Writing custom drivers can be difficult and time consuming, so try to leverage what's already out there. It may even be worth running linux even if you didn't plan to just to be able to leverage existing drivers.
Hope that helps.
Bob