If the program outputs FLAC the only lossy compression will be from the source stream, but it will pull the stream through your soundcard so there will be an analogue quality loss from there. The best alternative is to download the source stream, but when it can’t be done the second best is to record to a lossless format using whichever computer in your vicinity which has the hottest sound circuits.
FLAC and WAV are interchangeable when it comes to quality. The only advantage with WAV over FLAC is that it requires a tad less CPU to encode/decode (no practical difference), and the only advantage with FLAC over WAV is that you get smaller files.