I hear this a lot, but for my money, you will never convince me that Red Rocks isn't just the best DMB album (bootleg or commercial), but one of the best live albums ever.
There's a lot of good picks in this thread, but I'll add:
Prince - Small Club
Jaco Pastorius - The Birthday Concert
Sara K and Chris Jones - Are we there yet?
PHiSH - Slip, Stich and Pass
Earthless - Sonic Prayer
Bela Fleck & The Flecktones - Live Art
Derek & The Dominos - Live @the Fillmore
Grant Green - Live @the Lighthouse
Matisyahu - Live @Stubb's
Ween - Live @Stubb's
The Greyboy Allstars - Live
Built to Spill - Live