Fraser, unquestionably for mine - in Tests. Not by that much, but a clear mark there.
Both, of course, could have done so much more and were very probably only denied by injuries. The careers of both will always leave me with a feeling of great disappointment - as, I dare say, did those of Paul Reiffel, Damien Fleming and maybe even Jason Gillespie for the same reasons in Australian circles.
Fraser had one crucial thing that Gough never did - height. True, Gough could bowl both seam and swing (and swing with new and old ball - the first such bowler from this country to do so) whereas Fraser (especially after his injury) usually relied on there being seam in the surface to make him dangerous. But added to his height Fraser was much more accurate. If Gough were to get a ball that neither swung conventionally or reverse, he had neither the height nor accuracy (the former not helping the latter of course - taller bowlers have much greater margin-for-error in length than shorter ones) to be much more than fair cannon-fodder. Fraser was always at the batsman even if he didn't always offer to get them out - and of course, this meant that when there was something in the pitch for him he got far more wickets than Gough did because he hit the right areas so much more.
In ODIs, meanwhile, both were in their own ways quite brilliant, and the perfect pairing any captain could ask for. Fraser (and Caddick again immediately after his retirement) rarely failed to be good for 10 tight overs off the reel and very possibly an early wicket or two; Gough (until 2001/02 and his own problems starting) usually gave you 4 or 5 with a very high chance of early wickets, and then came back at the death and was often almost impossible to get away with his reverse-inswing and pinpoint Yorker length. Give either the other's job and they'd probably both go awfully - but you couldn't wish for much more if you gave them the right roles. So impossible to say one was better.