iTunes won't do FLAC files. But iTunes will do Apple Lossless (ALAC) files. These are very similar to one another and both are capable of lossless audio. So, you have two options, basically:
1. Use iTunes, which will require converting FLAC (or WAV) to Apple Lossless. There are several programs which will allow you to convert FLAC and WAV to Apple Lossless. If you want to use iTunes, this is your only option.
2. Use another audio frontend which can do FLAC files. There are several. MediaMonkey, WinAmp, foobar2000, VLC, etc.. There are ways to stream other players besides iTunes via Airplay. With Airfoil, for example.
Do some online research. There is plenty of info available out there.
"All men are frauds. The only difference between them is that some admit it. I myself deny it."