Closer to being comparable than Breaking Bad versus The Walking Dead, but in my opinion, much as I enjoy Game Of Thrones (and the books on which it is based, assuming I ever get to finish the series, which, who am I kidding, isn't going to happen,) Breaking Bad is still better.
ETA: A lot of the difference, in my opinion, is story arc and whether things are done for transient reasons. While both GoT and BB have/had a planned out story arc, the manner in which GoT improvises and changes things seemingly for short-term interest and ratings boosts detracts somewhat from the overall quality of the series as a complete story.
For a comparison using two other series, examine Babylon 5 versus Battlestar Galactica (not the original.) While BSG clearly had superior special effects, generally better acting, better budget, and some truly amazing stories and moments, the fact that the show was thrown together season by season and heavily influenced by ratings is obvious. While B5 suffered from having the planned 5 year arc cut to 4, forcing a lot of timing problems in the 4th season (and which resulted in the really better off forgotten 5th season after the folks who cut it off at the knees saw the ratings from 4 and decided to hand Straczynski a 5th season after all,) the overall quality of the story arc in its entirety made it the better program.