It goes without saying that Youtube's audio quality is quite bad, but sometimes there is material on there that isn't available anywhere else. In that situation, it's advisable to download the video at the highest quality possible. Once you have the video on your computer, convert the audio to a lossless format and perform the manipulations you want. Save again to a lossless format.
If you download a Youtube video, do a bunch of edits on the audio, then save as MP3 all you're doing is adding layer upon layer of data reduction on top of the already compromised signal.