If we assume this is in-game, then Thunderbolt all the way. It has a far higher base power, it's more accurate, and many 2HKOs will turn into OHKOs if you opt for that over Charge Beam. You should only use Charge Beam if you cannot get Thunderbolt for some reason.
Competitively, Thunderbolt is still better. The boost you can get from Charge Beam is not nearly as good as KOing opponents so much faster. This isn't to say Charge Beam is bad (though it really is, a lot of the time), but there's no reason to use it over Thunderbolt.
Here's an in-game set:
Magnezone @ anything
Ability: Sturdy
- Thunderbolt
- Flash Cannon
- Tri Attack
- Thunder Wave / Signal Beam
Hope I helped!