I would most certainly agree with David Gilmour on guitar, his tone is impeccable. And for someone with chops to die for, I'd add Danny Gatton on guitar - maybe the best guitarist ever...
Not quite sure what you mean by "boutique sound"; and, "best", as always, will be argued to be subjective. Having said that, I think that what you may be saying is that there are musicians whose musical "stuff" is so strong that the message always transcends and rises above poor recording quality. One can't polish a (musical) turd with boutique (?) sound enhancement; but, likewise, it's almost impossible to destroy the music in truly great playing with bad recording quality or playback.
As far as impeccable tone goes I agree with some of your choices, especially Heifetz and Clapton; and Getz, Frisell and Metheny for especially unique tones. Not so much with Haden or DeFrancesco. Haden was an amazing musician and one of my very favorite bass players, but I always found his "tone" somewhat diffuse and indistinct compared to other favorite bass players; no arguing with the music though. DeFrancesco makes me nervous with an over abundance of exuberance in his playing which, for me, detracts from his impressive tone.
Some musicians that, for me, define(d) the pinnacle of tone and are also musical masters:
Julius Baker (flute)
Robert Marcellus (clarinet)
Michael Brecker (tenor saxophone)
Horowitz/Bill Evans (piano)
George Mraz (acoustic bass)
Charlie Mariano (alto saxophone)
Jack DeJohnette (drums)
Manuel Barrueco (Classical guitar)
Obviously plausible arguments could be made for countless artists, but I'll nominate a few of my favorites in the vocal category:
Classical female vocalist: Dame Kiri Te Kanawa.
Pop/jazz/folk female vocalist: Judith Durham.
Classical male vocalist: Jussi Björling, Luciano Pavarotti.
Male vocalist (various genres): Paul Robeson.
Czarivey and all contributors, in the interest of keeping the thread relevant: please clarify what, exactly, we are talking about here? Many great musicians mentioned so far; but, are we talking about favorite musicians, great musicians, or, as your OP suggests, musicians with great TONE (not necessarily the greatest or favorite)?
James Ehnes gets my vote. The most astonishing phrase from a violin I ever heard was the soloist entrance in the Dvorak Violin Concerto by Ehnes. It was beautiful beyond (by a considerable margin) anything I have ever heard. I was seated about 15 ft from him. I just melted in my seat, and turned to my wife and she was obviously having the same reaction. I would give a lot to relive that moment.
I have a number of his recordings, and I treasure every single one of them.