Comparing these two hostgator with Godaddy will be like comparing apple with orange. They both are popular in the specific feild. As Godaddy is well known as most popular domain registrar and hostgator is popular webhost.
It's always a good idea to host your domains separately, i.e. away from the company you're using as your registrar. Godaddy is great as a registrar. I've never used them for hosting purposes, though. As for HG, I did once have a blog hosted on one of their shared hosting packages. Never tried their reseller hosting. I would recommend that you try it out for yourself if they have a money back guanratee. That way you can get your money back in case you choose to not continue with them.