Well, the general idea and opinion here is that Thundurus-T is the better of the 2, being as it boasts a better SAtk stat. But one will find that Zapdos has a niche in Heat Wave, and a better Ability overall. It is very controversial as to which is better of the two, but the true answer is none of them are better than eachother overall. Here's why:
Thundurus-T is better than Zapdos if and only if you compare them both as Special Sweepers, while Zapdos is better than Thundurus-T when running a SubRoost Moveset/Defensive role.
Don't know why I put that in quotes, lol. Anyway, if you are considering running more of a Scarf/Offensive role, consider Thundurus-T over Zapdos, but if you want a Rain Team with a Ferrothorn counter, or a more Defensive Pokemon that packs a punch, roll with Zapdos.