CE Rob Landry put a ton of time and effort into maximizing the audio quality of WCRB 102.5 for many years before the sale. The result was impressive...whether you liked WCRB's choice in classical, the audio quality was quite good. That Inovonics Omega FM processor was sweet. I have no idea how much of that equipment migrated to 99.5...hell I don't know if Rob migrated himself. He's an excellent engineer, though...a real "golden ear".
WERS has historically put in a lot of effort to have a quality airchain and transmitter. IIRC they had an Aphex 2020 that also sounded quite nice. Again, with the new HD transmitter I don't know what they've got in there now. The same guy helps maintain WHRB's transmitter plant so I assume their STL & processing are of good quality. Their air studio is pretty elderly, though.
But of all the stations in Boston, I'd say WBUR is the most meticulous about their studios, airchain and processing. Considering that a lot of their audio goes through multiple codecs thanks to the new ContentDepot satellite system that PRSS uses, it still sounds quite good. I'm listening to them right now and the HD signal sounds excellent. Actually WBUR's shining achievement is their processing...which does an incredibly good job of making every speaker sound at about the same "loudness" regardless of the source quality (studio, satellite, ISDN, telephone, cellphone, satphone) so you rarely have to struggle to understand the speaker, nor do you have to adjust the volume very often. The only place I find they have problems with that is the BBC World Service which is a lot more accepting of terrible audio quality than NPR usually is. There's good reasons for the BBC to be like that...but it's still maddeningly difficult to understand some of the phone calls they air.
On the bad end, I have heard WTKK air MP3's that couldn't have been better than 16kbps mono and they sounded gawdawful on analog, I can't imagine on HD. And the processing on WBCN & Kiss108 used to be unbelievably aggressive, to the point where you could clearly hear the compression going on. I wonder if they've backed off since HD was installed?