It's a toss up (ha). 94 potential base damage against 90 potential base damage. HTA's have a higher chance of one-shotting or black-barring low to medium armor opponents, Hammers give more ammo and will fare.. fairly.. against any target. I'd say that axes have the edge, but only slightly, provided you can hit your targets reliably well with either.
I'd probably go with Hammers, Stones, War Darts, or Throwing Lances as a thrower, personally. Just my preference.