How can you consider that obvious??

Starscream asserted his authority over Shockwave at least twice, but times Shockwave fell silent.

 

I think it depends on which version of the fiction you're looking at -

Toon: Starscream. Shockwave does abdicate to Starscream in "Countdown to Extinction" which indicates to me that in the cartoon hierarchy, Starscream was in fact senior. You never see Starscream kowtowing to Shockwave the way he does to Megatron, an obviously more powerful being.

Marvel: From what I'm reading here, and the little I remember of the comics I had - definitely Shockwave.

And if there was no cartoon or comic, and we're going off the titles listed on the toys themselves - much as I hate to say it, it would be Shockwave. The title Military Operations Commander is pretty specific - the position of Air Commander would be subordinate to him.

I tried to rationalize this to myself by arguing that perhaps shockwave is nothing more than than Megatron's S3 (Operations Officer), but he's not an operations officer - he's the commander which pretty much ends the discussion. And also my attempts to apply US Army command structure logic to the Decepticon hierarchy  

 

100% reasonable.

 

As much as I think Shockwave is awesome I'm pretty sure Screamer is second in command. Whenever Megs isn't around he is in charge and he is always trying to kill Megs so he can be leader. Shockwave is just stuck on cybertron so can't really be second in command. And for those wondering why Megs would have someone he hates as his second in command well that's because Megs realizes Screamer's skills as a warrior.