If they are bomber spamming massing carriers carrying fighters will do(fighters counter bombers) it. Add in some light frigates(light frigates are the best at killing the source of the strikecraft the carriers themselves) to actually hunt the carriers if you're still at a stage of the game where they won't just feed the enemy titan.
Once titans roll out if you use light frigates and how you utilize them will depend on the titan(in this case your first priority is avoiding feeding the LF to the titan- actually killing the carriers is second priority)- unless your confident of your ability to micro them and understand what sort of zones each titan threatens thought using them is risky(would be safer to just mass carriers with bombers or fighters yourself).
If you're advent, the Steal Antimatter ability can allow your Light frigates to quickly deprive the carriers of antimatter(preventing them from rebuilding destroyed strikecraft)- which can effectively remove the carriers from the fight much quicker then killing them, allowing the LF to quickly do their job then flee from the wrath of any nearby titan. Of course any LF fleet will need to be accompanied by flak(if the enemy has a lot of fighters) or fighters of your own(if the enemy is massing bombers- Preventing reinforcements isn't worth much unless you can kill the initial complement of strikecraft.
Ant-SC abilities help as well. in particular TK-push for the advent(on the Halcyon) and Weapons Jam on the Kprtul(vasari are great for buying time to kill the strikecraft. The Vasari's defenses also sport the phasic trap which is hugely useful, if only usable defensively.
The TEC are a bit lacking in anti-SC, their only dedicated tool being the hail-mary of building a few Kols(usually a bad idea) for flak burst. Honestly the biggest actual advantage the TEC have at antiair is the Akkan's Targetting uplink, which makes flak in particular a lot more effective(more range & negates the inherent accuracy penalty of attacking strikecraft). But this is more handy for killing fighters then bombers since it affects your flak but not your fighters.