First a special mention for Henry Threadgill who has had a long and distinguished career. His Sextet(t) started out on the obscure About Time label and I'd single out Just The Facts And Pass The Bucket (1983) from this period. The three Novus albums which came later are all very good as well. His next band was Very Very Circus, try Too Much Sugar For A Dime (Axiom, 1993), very exciting indeed (but you have to like guitars). His most recent stuff has been with Make A Move eg Everybody's Mouth's A Book from 2001 on Pi.
Also from Chicago (the jazz town) Ernest Dawkins' New Horizons Ensemble lay down an irresistible blend of up-tempo rhythms and virtuosic soloing on albums like Mean Ameen (Delmark, 2004). Then there's the Vandermark Five, one of the many projects of reeds wizard Ken Vandermark - their latest double CD The Color Of Memory (Atavistic, 2004) is outstanding. Percussionist Kahil El'Zabar has worked in many contexts including the Ritual Trio and the Ethnic Heritage Ensemble - for sheer enjoyment I'd recommend Love Outside Of Dreams (Delmark, 1998) by his trio featuring David Murray.
Some more:
Leo Smith Golden Quartet The Year Of The Elephant (Pi, 2002)
Roy Campbell Ethnic Stew And Brew (Delmark, 2000)
Revolutionary Ensemble And Now... (Delmark, 2004)
William Parker/Little Huey Creative Music Orchestra Music For The Healing Of The World (Black Saint, 1998) - a great sprawling behemoth of a big band which I find utterly exhilarating when on top form (which is often)
Dennis Gonzalez' Spirit Meridian Idle Wild (Clean Feed 2004) - Gonzalez is a fine trumpet player from Texas, and Clean Feed is a WAY COOL new label out of Portugal
Finally, if you want to hear the Art Ensemble in cracking form but a slightly different (bluesy!) groove, try their double CDR Salutes The Chicago Blues Tradition, available direct from their website.
Jim