Weeeeeell... let's think.
Thunder makes the most incredible of incredible damage, but only hits 7 out of 10 times. So it's a 30% chance it will miss. That's pretty high, yet possible.
Thunderbolt is a move that always hits, but does 95 damage.
Imagine adding the two moves' accuracy and damage together:
Thunder = 120 + 70 = 190
Thunderbolt = 95 + 100 = 195
Yes, Thunderbolt wins, but as much as my inner-self wants to scream Thunderbolt, I actually go for the opposition.
I have had my history with Thunder, and most of the times I've used it, it has hit.
What I did was that I taught my Ampharos Shock Wave and Thunder, so if Thunder is always missing I can hit them with Shock Wave. Substituting Shock Wave with Thunderbolt, and that's a great technique right there! (But it wastes half of your moveset D:)
I would personally recommend Thunder, because if all goes well, your opponent will be begging for mercy. However, I'd recommend a back up move, in case your luck isn't very 'lucky'. Shock Wave, or Thunderbolt are good options.
Sorry about the wall of text, I do this a lot. xD
Hope I helped somehow :)