A USB2.0 connection is sufficiently fast enough to saturate any wireless link, even a 5.8Ghz 802.11n link, so it comes down to antenna performance, and a pcie board with external antenna is likely to perform better UNLESS it's antenna position is compromised by position relative to where the USB dongle is (eg if the dongle is up front with a more direct path to the access point or router, and the pcie is behind and has only an indirect path.
Both devices are power limited by the FCC, and a USB port can easily supply sufficient power for most transceivers to be non-power limited, so it then depends on the amp in the dongle. (as the pcie can likely use a more powerful chipset due to relaxed space constraints)