It really depends on what you are going to use those album covers for.
If you are going to tag your mp3 files with cover images, I wouldn't use images larger than approx. 60 kB or approx. 350-500 pixels (whichever is smaller). This is in order to ensure compatibility with some devices.
If you are going to use the cover art for printing new covers later on, it makes sense to have good quality high resolution cover images. I wouldn't insert those large images as tags in the mp3 files, however, but instead tag with a scaled down version.
EDIT: Just noticed you were talking about FLAC files and not MP3 files, so the limitation I listed on cover size may be irrelevant.