In the beginning, mining. Copper > Silverleaf/Earthroot/Peacebloom.
In the early middle (level 20+), herbalism. Swiftthistle and Kingsblood > Tin.
In the middle (level 30-40), it depends. Iron is great, but herbalism has a lot of easy-to-find herbs that, while they sell for less, are very prominent.
In the later middle, mining, but just barely (level 40-48ish). Mithril and lots of Iron (very easy to find at this level), and the very rare Dark Iron for the adventureous > Sungrass (though it is still decent) and the rare Ghost Mushroom (VERY rare).
In the end-game, tied by luck. Mountain Silversage/Plaguebloom/Dreamfoil > Thorium any day, every day. But if you find an Arcane Crystal/Blood of the Mountain, you get a major income boost (dozens of gold more). If you're lucky, mining > herbalism; but not counting luck, herbalism > mining.
Hope that helped! ^_^