Both helicopter and small-plane scenic flights run from Franz Josef daily, weather permitting. The standard helicopter trip flies over the glacier and the upper névé snowfield, with a brief landing on snow at the head of the icefall. The fixed-wing flights — slightly cheaper — fly over both Franz Josef and Fox glaciers and on across the Main Divide to Mt Cook / Aoraki, returning by way of the West Coast.
If you only do one flight, the Mt Cook flyover is the more spectacular: glaciers above, snowfields stretching to the eastern slopes, and the great north face of Mt Cook itself. Both options depend heavily on cloud, and flights are often delayed or cancelled in this very wet part of New Zealand. Book early in your stay so you have a fallback day if the weather closes in.