Well first, let's look at their stats.
Altaria is more defensive with 75/90/105 bulk and mediocre attacking stats, while Salamence is more offensive, with 135 base Attack and 110 Special Attack. As playthroughs are more offensively oriented, Salamence wins here.
Now let's look at availability. Altaria can be found as a Swablu on Routes 114 and 115. It then evolves quickly at lv. 35. They are much more common than Bagons, which are in the back of Meteor Falls and require you to get the HM Waterfall. Bagon evolves into Shelgon at lv. 30, and Salamence at lv. 50. Altaria is the better choice in this regard, as using Bagon will mean a lot of grinding.
Both Altaria and Salamence have decent movepools, but Salamence can make more use of great moves like Earthquake, Fire Blast, Fly, Dragon Claw, and Brick Break due to it's large attacking stats. Altaria can also learn these moves (with the exception of Brick Break) and tacks on stuff like Solar Beam, Ice Beam, and Perish Song.
Altaria gets the ability Natural Cure, which is nice, but not as useful as Salamence's Intimidate.
I personally would use Altaria for more ease of play, but if you're not scared of grinding and long Pokemon hunts, use Salamence. Salamence is better overall.