There is no best server, it depends all on your requirements, maybe you would want to evaluate your requirements and see which fits your needs. No one can answer this question better than yourself.
I wouldn't use either, find a normal hosting company that isn't mainly a web portal or a domain registrar. Hostgator are very good, but quite expensive. I can give you a server if you PM me. But if not, then go with hostgator.
i was doing fine with godaddy... and felt contented at first.. until an idea of having a video site pops up because of the youtube clone trend.. i was able to stumble on hostgator... i must say... Godaddy's support is good.... but hostgator was definitely awesome.... almost on the same price range...
Out of them I would choose hostgator anyday, because they are actually a web host. Buying a server from godaddy would be like buying a car from a fish and chip shop.