You're going to get the same update by doing it over the air or on iTunes. The difference is that iTunes will require less free space on your iPad to do the update. I had to open up about 5 or 6 GB of free space to complete the operation of updating to iOS 8.1 from iOS 8.0.2 ...
However, you might want to do a "clean system install" and that's when you use your iTunes program to reset your device to factory default condition ... and therefore you are not installing on top of an older system, but are installing it "fresh and clean". You might do that, and no matter what, this kind of install will produce the best results possible, with any upgrade!
Here are some Apple Support documents for backing up your device, so use your iTunes program to do that. The last link shows you how to do a reset to factory default by using iTunes.