geofelt :
A hot swap bay will run at sata speeds, much faster than usb3.0.
In theory - this is correct. In practise either USB3 or SATA2/3 have far more available throughput than the mechanical HDD they are connected to.
There are differences in SATA2/3 and USB3 overhead - but a different HDD will probably have a bigger performance difference than choice in interface.
That said I'd suggest the external USB3 drive as it is one piece, has the HDD enclosed, if using a 2.5" drive is powered over USB, and can easily be taken to any other PC to share files - while the hot swap isn't easy to move between systems or requires opening the case to connect the HDD to share files.