Well, let's look at all of the aspects of each.
Mega Manetric is an Electric type and gains the ability Intimidate upon Mega Evolving. It has 135 as both its base Special Attack and Speed stats, and gets 70/80/80 bulk.
Its movepool is pretty good too, with Thunderbolt, Flamethrower/Overheat, Volt Switch, Charge Beam, etc.
Intimidate works as a good ability to counter Earthquake, the most common move used against Electric types. It also makes Manetric a very good counter for Talonflame. It can be very good as a lead if you teach it the right moves (i.e. Thunder Wave, Thunderbolt/HP Ice, Overheat, and Volt Switch).
Mega Houndoom has its own perks. It's a Fire/Dark type and gains the ability Solar Power when it Mega Evolves. It has a 140 base Special Attack and 115 base Speed, and gets 75/90/90 bulk.
It has a good movepool as well. Its typing, while giving it more weaknesses, gives it better coverage, and Houndoom gets access to Nasty Plot, so it can be a great setup sweeper.
Mega Houndoom is utilized best when in the sun and makes a good revenge killer, if you have the set for it (i.e. Nasty Plot, Flamethrower, Dark Pulse, and Solar Beam).
So to get to the point, it's honestly up to you which one you choose. Mega Manectric works better as a lead, but with sun support, Mega Houndoom is deadly. In most circumstances I'd go with Manectric (due to the fact that you probably don't have a sun team), but either one works great.
Hope I helped!