Ironically, updating to iOS 6.0.1, at least for now - seems to have made WiFi sync more reliable for me on my iPad 3, and my MacBook running OS X 10.7.4 and the latest version of iTunes.
if you have quit iTunes, rebooted your devices and restarted the computers and that didn't help, this is what I would suggest next ... And in no particular order.
Turn WiFi off on your iPad, restart it and then turn WiFi on again.
Try rebooting your router. Even though you may have Internet connectivity with all devices, rebooting the router might just work anyway.
Connect the iPad to your computer and launch iTunes, select the iPad under devices, click on the Summary Tab and uncheck Sync this iPad over WiFi. Click on Apply in the lower right corner. Sync your iPad. After the sync completes, go back to the Summary Tab. Click on Sync this iPad over WiFi. Click on Apply and wait for the changes to be applied. Quit iTunes and disconnect the iPad.
Restart your computer, launc iTunes again and see if it works now,
For me, the upgrade to the latest version of iTunes - and then updating to iOS 6, made WiFi sync extremely unreliable. In my case - iOS 6.0.1 seems to have fixed it.
You can try resetting all settings on the iPad. Sometimes that can fix a setting gone bad (WiFi sync in this case) and it can clear up certain unexplained issues. Settings>General>Reset>Reset All Settings.
If you try this you will have to enter all of your device settings again.... all of the settings in the settings app will return to default settings.
Alright, it seems as if the problem might be that there have been some changes regarding wifi that were not in the ios6/itunes combo. The only time that the unit will sync on wifi is if it is plugged in to the charger. It will not sync at any other time. Otherwise, it has to be connected to the computer (mac or otherwise). The older version would allow a sync from itunes even if the unit was not plugged in. Does this make sense?