Are you discussing an FPGA design with embedded software to run the FPGA design (Cyclone V DE1-SoC) or a software solution on a Raspberry Pi 3? If you are only using the Cyclone V's dual core A9 then this question doesn't even belong in the FPGA section.
As you are considering a Pi3 instead of the SoC solution then you probably had no intention of using the FPGA fabric for acceleration, so which one is "stronger" (a poor choice in terminology for a processor performance metric) is boils down to use which ever on has the most memory, fastest RAM, and highest clock speed (same as when you go buy a PC).