Could also do square-pin header, that's just over-long, and use thru-pin (stackable) sockets to mate it. Heh, assuming the boards can be stacked axially, of course this wouldn't work so well if they're slid in separately or something...
What EMI environment is this like? Is the surrounding structure just plastic, or does it provide any shielding/grounding? Do both boards have cables attached or anything?
Putting USB over open, unshielded connections like these (ribbon, FFC, pin headers, etc.) is a bit iffy. It may be desirable to add a ferrite bead or something, or shielding (which can be a foil backing, if it can be mated to both boards), or extra grounds (to the same end, just around the boards, rather than around the cable). Or extra filtering if it only needs to be USB Full Speed (12Mbps), not High Speed; not really great, but it's a little something.
As for the cable, both for bend radius and for ease of assembly, I might suggest using horizontal connectors, preferably near the center of the boards if that space is available, so it's facing out and accessible. Bend radius should be in the datasheet, if not it's typically 5mm or something like that?
Tim