Yep, mini-B. The micro-B seems to be getting popular, but it just doesn't seem strong enough to me.
One reason manufacturers seem to favor micro-B is that the "teeth" are on the cable side of the connector, which is easily replaced by the user; mini-B has the teeth on the device side, so broken teeth require the manufacturer to repair/replace the device.
Probably not as important here unless users plan on plugging and unplugging their FPGA boards a lot.