My wifes 09 HHR 2.4,42,000 on engine,makes a odd noise after the engine runs for a few minutes.We thought it was possible the alternator,so I removed the belt and started it and same noise.Any ideas?

 

With that vague a description, my only guess would be a cracked flex pipe.

 

with our stethoscope the noise sounds louder in the valve cover on the timing chain side which seems to transfer to alternator.

 

A thump, bump, squeal, tick, knock, grinding, real loud, not loud, howling, screeching, etc. etc. ?

Honestly, without some kind of description of the noise, I'm not even going to take a guess.

 

it makes a whinning sound at idle and noise goes away at about 3000 rpm.Almost sounds like a convertor whine except its in the engine.

 

Pull the valve cover , check the timing chain guides and tensioner.

 

took it to dealer today and called gm customer service.

 

Let us know! Oh, another thought, the air filter box bracket

 

Called GM customer service ???
There must be some details that the OP is leaving out. Never heard of someone taking their car in for a noise AND calling GMCS at the same time. Why would a 7 year old car deserve a call like this ?

 

The problem is the water pump.