The Noctua runs cooler at both idle and load but no more than 5C and it's also noticably quieter [by like 7db]. The Noctua is clearly better performance but you didn't list the prices. You have to decide which one is worth the money. Personally, I would go with the Noctua if the price difference isn't much.
The price difference is like $30. I would say it's money put to good use if you want a quiet system. Here's the links: http://www.guru3d.com/article/cooler-master-v6-gt-review/10
http://www.guru3d.com/article/noctua-nhc14-cpu-cooler-review/9
IMO the NH-C14 is way over-priced compared to better HSFs. It does appear to be better than the V6 gt but for less money I'd go with the Xigmatek Aegir SD128264 which performs better on AMD CPUs and costs less than the C-14. See the links below as HSF performance varies with CPU model/brand due to heatspreader area.