All the goals came in the opening 21 minutes, with Kevan Hurst and Gary Hooper giving the hosts a two-goal lead.
Michael Raynes' header halved County's deficit but Gannon's side could not find an equalising goal.
Stockport are eighth and four points adrift of the play-off place, having played more games than many of their rivals.
"We are going to have to put some wins together now if we are to gatecrash the play-offs," said Gannon. "We've got some young lads here who I think will one day go right to the top. They face a difficult period over the next few weeks but it's one they will both learn from and benefit from for the future.
"We've got to try and put behind us our off-the-field problems. When a business is in trouble all you can do is your best and hope that the business will benefit from that. We've had to throw in some kids this season and they've been magnificent."