Right now there seems to be some unity between the three, so I can't tell which is the best. Like it's random enough you never know the best way to get the best weapon, just keep playing, looting and looking at traders, and craft when you can craft something better than what you found. The harder biomes have better loot so go to the wasteland for the best possible loot, if you dare.
Oh and I forgot to mention, but you can find the type of magazines you are after also by looting an appropriate type of crate. For example gun crates have gun magazines, pop n pills crates have medical magazines, mo power has tech mags, etc.