Yes, you can shoot projectiles and grenades using V.A.T.S.:

Projectiles can be shot out of the enemies hands or while they are being thrown.

You can definitely shoot grenades out of the sky using V.A.T.S. as I've done it - you can also shoot the mini nuke carried by suicidal Super Mutants as they're running towards you as an easier method of killing them. It would be logical that this also extends to mini nukes in flight as they're projectiles*.

^{* I'm saying yes you can this very second but I'm going to test it tonight}

Yes, you can shoot projectiles and grenades using V.A.T.S..

You can even shoot the mini nuke carried by suicidal Super Mutants as they're running towards you as an easier method of killing them, but as it's probably better to kill them without detonating the mini nuke so you can loot it!

You can definitely shoot grenades out of the sky using V.A.T.S. You can also shoot the mini nuke carried by suicidal Super Mutants as they're running towards you as an easier method of killing them. It would be logical that this also extends to mini nukes in flight as they're projectiles*.

^{* I'm saying yes you can this very second but I'm going to test it tonight}

Yes, you can shoot projectiles and grenades using V.A.T.S.:

Projectiles can be shot out of the enemies hands or while they are being thrown.

You can definitely shoot grenades out of the sky using V.A.T.S. as I've done it - you can also shoot the mini nuke carried by suicidal Super Mutants as they're running towards you as an easier method of killing them. It would be logical that this also extends to mini nukes in flight as they're projectiles*.

^{* I'm saying yes you can this very second but I'm going to test it tonight}