I pretty much have the same strategy. I think the only way to get those flying bosses is to have a hell of a lot of firepower combined with very powerful freeze towers. It also helps to not have any other enemies on screen at the time as well, or at least none that are within range of the towers that are focusing on the fliers.

But frankly, I don't know. I can usually stop the one flying boss in easy mode, but I haven't stopped the ones in medium or hard.