My vote is for the Dead. Garcia/Lesh had a synergy that was other worldly. "Hollywood" Bobby Weir filling in the spaces between Jerry and Phil.
The original New Riders of the Purple Sage with Dave Nelson, John "Marmaduke" Dawson and Buddy Cage, sometimes joined by Garcia, Lesh and Hart were an outrageous guitar band. Not everyone's cup of tea musically, but a boat load of talent.
The newer David Nelson Band is very enjoyable, with a lot of very proficient guitar interplay between Dave Nelson, Barry Sless and keyboards (w/ occasional guitar) of Mookie Siegel.
Duane Allman/Dicky Betts/Barry Oakley combo are right up there in my book as well.
Both Phil Lesh and Barry Oakley play(ed) with a style that turned the bass from a backbeat foundation to an upfront lead melody machine.
My user name is taken from one of my favorite Dead tunes: Slipknot!
usually put in as part of Help On The Way>Slipknot!>Franklin's Tower trilogy in live shows. Probably explains my vote for the GD as the greatest guitar band ;)