I've only been in a helicopter once and I wasn't taking pictures so I don't have much to add that David didn't already cover.

Definitely go with the 24-105 as it has IS. You didn't specify which 70-200 you have so I'll assume it's not one of the IS models. The 24-105 is more compact so it will be easy to manoeuver and hold steady in a helicopter. It's harder to hold a long lens steady against a window when you are moving.

Use a polarizing filter if you have one. It will give you better contrast on the landscape and help cut down on any internal glare from windows, the latter being more important.

The 6D has decent high ISO performance so you may want to crank it up to 400 or more just to make sure you get a good shutter speed. I think Auto ISO should work just fine. This is especially true if you use a polarizing filter as you will loose one or two stops.

Have fun and post your results.

__________________
Wake up every day that would be a start.