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,