Flightseeing is always expensive, no matter where you go. Between a high overhead for the tour operator, and no doubt very high insurance prices for his business, it's no wonder. If you really want to do Alaska shore excursions "on the cheap," it's one of the best places to just get off the ship and walk around the ports. No language, signage or currency barriers.
If it's your first time in Alaska, though, I'd recommend some of the tours to the natural or cultural sights, such as Mendenhall Glacier in Juneau (not flightseeing, just the land-based tour), Saxman native village in Ketchikan (totem poles), and perhaps more spendy (but worth it) the White Pass RR in Skagway.
Less expensive in Skagway and also fun is the yellow-bus tour (the old 1930s stretch vans, imported to Skagway from Yellowstone & Glacier NPs way back when). The gals giving those tours dress in turn-of-the-century costume and are enthusiastic & energetic (and impressive drivers - you should see some of these old vans!)