I'm sure you've checked already, but take a look at the allowed baggage dimensions for different airlines, as well as charges for bike boxes. Right now it seems as though smaller airlines, such as Allegiant Air, Mesa, and Alaska Airlines, are still around $50 each way for bike boxes. The major airlines (Continental, Delta, United, etc) can charge up to $150 each way.
If you decide to take the bike box option, here's a link that might help that process go smoothly: http://www.adventurecycling.org/features/boxingbike.cfm
As far as insurance goes, I'm afraid I don't have an answer for you, but you can take precautions by putting 'fragile' tape on the bags before checking.