Both are using a GPU made by nvidia. And while they do build the circuit boards, usually it's form the same parts suppliers.
Sometimes there is 'binning' of the GPU's, saving the better performing GPU's (silicon lottery) for the OC and superclocked versions of a card. And some companies are better at binning than others. Also some companies have better quality control.
I've had both MSI and EVGA cards fry on me. More than one of each actually. In my experience EVGA is not better made. If the price is the same, i'd go with the EVGA though for the extra overclock... or whichever has the better warranty... or check youtube for noise comparisons
Personally I'm delighted with my Gigabyte G1 Gaming. Runs very cool, never gets too loud, OC's like a boss (good binning i think), and seems well built. Granted, i've only owned it for 7 months, so I can't speak to how well it holds up over time.