Vicks7,
J&R has an excellent selection of CDs and a decent supply of SACDs ... at some of the best "New" prices in NYC. Virgin also has a very good selection, but at higher prices.
Kim's on St. Marks has one of the better selection of "Out" and independent jazz, including European improvisors and a decent selection of used cds.
If you are predominently interested in used jazz CDs, Academy on 18th, between 5th and 6th is one of the best. They do not, however, have many SACDs.
Finally, Downtown Music Gallery at 342 BOWERY, between 2nd and 3rd is actually mostly jazz (mostly new, but with some used), with a special emphasis on more experimental music ... especially of the "Downtown" variety.
