Are they running IOS? If you have any unix/linux command line skills check out RANCID. It comes with an application called clogin which will help you to script logging into and entering commands in the Access Points including making config changes.
If that doesn’t work you should look into Cisco’s Wireless Lan Controllers. You would need to run the Light Weight Access Point Protocol on the APs but then the controller would enable you to administer all your APs as a group.