It really depends on what you're looking for. In Juneau you will get a really good glacier flight by helicopter. In Ketchikan you are at the start up point for Misty Fjords, a magnificent wild area, already glaciated, with waterfalls falling hundreds of feet into the fjords below. On some of the flights (by plane, not helicopter), you land in a mountain lake where there is no other sign of humanity other than the plane and it's human contents. It's an utterly magnificent flightseeing tour. It is one of Alaska's high points for me.
Carole