Depends what kind of action I want on that given day. (Based on split shot rigging which is what I use through the ice)
For most mobility of the minnow, just behind the dorsal fin is best. This allows the minnow to swim in a full circle around the shot, depending how far your lead is from your shot it can be up to 2 - 3 feet. I usually go about 6 - 8 inches though. Good for active pike and the evening crappie bite.
For a move, stop, move action, I hook just in front of the tail of the minnow. He'll swim for a bit then drop dead.. great for pike and crappie.
For a stationary wiggle, I hook the minnow through the eyes. I find this best for perch however you have to make sure there's a good delay before you set the hook. Through the eyes the minnow can last over an hour.