I have no experience with PCIe, but USB has two features that might be useful:
1. Hot plugging. You can connect and disconnect your device at any time so (i) if you need to fix something in hardware, you don't have to reboot your computer, and (ii) by disconnecting the FPGA (and turning it off if it has external power) you reset it's state, which may be harder to ensure on PCIe.
2. You can write driver in user space by using libusb. Or so I've heard…
Never tried it myself.
So if I were you, and adding USB interface to the FPGA chip was not a problem to me, I'd use USB.