Well, Magnteon and Ampharos have much differnet things to consider since we're talking about Gen 2. So, I'll give you my version of a breakdown, based on who I think is better
- higher Sp. Atk
- much faster
- not a big move pool
- no STAB moves for it's steel-typage
- better defenses + HP
- better move pool
- better resistances
In concern to Magneton, you might prefer it if you want a fast sweeper. Normally, you wouldn't consider Magneton being your fast Pokemon in your team, but it this case, it would. Magneton has great electric STAB moves such as Zap Cannon (base 100) by level up, or Thunder (base 110). However, the rest of it's attacking electric moves (only one) only have base 40 (Thunder Shock). The rest of it's attacking moves are Normal type, excluding Rollout learnt by a TM. So, in this case, you might wan't to use of the rest of its move slots with Thunder wave, Toxic, or Lock-On to help with Zap Cannon - but Lock-On won't be ideal since it has less accuracy, and is weaker than Thunder. But, if you do decide to use it, you can replace Thunder Wave with a Normal move or Rollout, since Zap Cannon causes paralysis.
In conern to Ampharos, he would definitely be a tanker in your team. Ampharos can learn a lot of better moves such as Thunderbolt and/or Thunder punch to cover it's only STAB typing, electric. It can also learn other great typing moves such as Fire Punch, Dynamic Punch, and Iron Tail via TM. However, with it's lower Spd. and Sp. Atk compared to Magneton, you might find yourself needing a few turns to defeat one Pokemon, so you would need to rely on an Ampharos with good Def, Sp. Def, and HP IV's. It can also learn great status moves such as Cotton Spore and Toxic, as well as some good outside-battle moves such as Strength, Flash, and Rock Smash.
Overall, I would chose Ampharos > Magneton because it's summary does seem more sensible and appropriate to any situation in comparison to Magneton, and trainers still appreciate Ampharos and Magneton - so it's your choice!
Good Luck Picking! Hope I helped! :)