App data is contained within the apps in iTunes, without a doubt. What you need to make sure of is that the apps have synced back to your computer from your iPhone, so that it is the latest version of the app. Usually this happens after you do an on-device app update automatically, not sure exactly how you can manually do it. I'd say delete the apps off of your computer, then have "Transfer Purchases" from your iPhone. That will bring the on-device version of the apps along with their AppData over to iTunes.
Originally Posted by Ipheuria
Hope I helped!