As shaten has so concisely put it, Flying Monstrous Creatures do not get the option to select skyfire for a round (unlike flyers), so flying shooting is no more reliable for us against flyers than the rest. Shaten also puts his finger on why selecting fortifications is a no-go: according to the FAQ, Tyranids, not having the spare opposable digits, can't operate weapon emplacements.
So our best option, I would say, is probably to stock up on lots of devourers with brainleech worms. A single Hive Tyrant rocking those bad boys can expect, on average, 3-4 hits per turn. At strength 6, against most of the flyers I'm aware of, that likely leads to about 1 or 2 glances per turn, depending on what armour facing you're going for (AV12 of course your odds decrease a lot. Any flyers with AV12 all over the shop?). So with not a huge amount of luck, a single MC with 2 x brainleech devourers should be able to glance a single flyer to death. Take 2 or 3 such monsters (Carnifex work just as well) and you should be able to put a significant dent in your opponent's flying cohorts.
It's no sure fire thing of course, but it has to be said that there are a LOT of other races with similar, if not worse problems. Sisters of Battle, for instance, will have serious issues shifting flyers unless they take an allied flyer themselves. We don't have the best kit to deal with flyers in the game (cough cough Hydras cough), but it is doable.