I found that the easiest way to kill the Hydras when they're in the air, by far, is with the Black Widow gun. All you have to do is fire the grenades at the Hydras, when they're in the air, of course, and detonate with the X button. Try to anticipate the paths the Hydras will travel in their "flights" and correct your aim as necessary. Takes about one to two grenades, depending on your accuracy.
I would also recommend finding an area with a Hydra(s), killing him, and then killing yourself to reload your checkpoint. This way you can get the achievement out of the way without having to worry about ammo. A checkpoint is usually made at each little battle - check first to make sure you won't spawn too far behind. The kills are cumulative; they keep score even if you die without a save.
Have fun.