1. Penetrate into it with a bomb that releases all kind of explosive force down into the fortified structure

2. Shake the earth so much that everything collapses

Ground penetration might seem like the obvious choice, unless you think it might fail to penetrate. If it fails to penetrate, you might shake the earth enough to collapse bunkers, BUT you will also kick an enormous cloud of sand and dirt into the mushroom cloud, where it will mix with the isotopes being formed up there before landing on the ground again. That means it's going to be hazardous for anyone to enter that area and see if there was any damage. If you do an airburst, any residual radiation will float harmlessly into the atmosphere, AND you can use larger yields.

Conversely, it may be possible to use ultra low yield nukes that emit ion flux deep into the earth. This is because the range of the ion flux (the "prompt" effect) varies inversely with the range of the explosive force. It's counterintuitive, but the ion flux will penetrate sand and steel bunkers and destroy all cellular life and all electrical equipment inside, no problem.

(http://www.autoadmit.com/thread.php?thread_id=5737712&forum_id=2#49025400)