Quite honestly, there is almost no difference between the two of them in terms of raw strength. Yamcha seems more skilled in general with his Ki, what's with being the second character after Goku to master the Kamehameha (and later creating his own unique technique, but that's for another debate).
However, as pointed out by CC, Krillin's ability to think outside the box definitely is a quality he has over Yamcha. And if the two had the chance to fight, Krillin would have most definitely win imo, since I believe it's a more important quality to have in a battle than firing a better Kamehameha, particularly when it allowed Krillin to win against an opponent who had far better techniques.