Of the two, the '06 will burn more powder to get roughly the same energy as the 260rem. As you mentioned, finding heavier 6.5mm bullets is easier than finding heavy .257" bullets. Bigger case capacity of the .25-06 with a proper powder should be able to push a bit more energy out than the .260rem, but the difference won't be huge either way.

Personally, I'd throw the .243win in the mix since you mentioned antelope and groundhogs. Even for whitetails, I'm more and more convinced that the .243win is the optimum whitey cartridge.

Out of your two, I'm a bigger fan of the .25-06 than the .260rem, but flip a coin, you'll be happy.