Depends on what type of Special Attacker you desire.
Zapdos' offensive movepool isn't exactly the greatest. Notable moves are probably just Heat Wave, Hidden Power, Thunderbolt, Extrasensory, and Volt Switch. However, for a bulkier special attacker, you can definitely go for Zapdos, as it supports superior bulk. It even has access to Roost, which allows it to recover lost HP. In addition, Zapdos has Defog, allowing you to clear hazards if it becomes problematic.
Thundurus' offensive movepool is impressive compared to Zapdos: Hidden Power, Thunderbolt, Volt Switch, Focus Blast, Psychic, Dark Pulse, and Grass Knot. Thundurus' speed surpasses Zapdos' by 11 Base Speed, giving it a better offensive presence. In addition, it can boost its Special Attack using Nasty Plot, something Zapdos lacks. One more impressive thung about Thundurus is that it has access to Knock Off and Superpower, allowing it to lure the counters of normal Thundurus (Blissey, Tyranitar, Chansey) and take them out with the appropriate move, making mixed Thundurus viable. However, it is much frailer than Zapdos and has no access to reliable recovery.
td;lr:
- Zapdos for a bulkier special attacker / support
- Thundurus for an offensive special attacker
