In the interest of full disclosure I must note that I have been involved with KFJC 89.7 FM since 1989, so, obviously, I am biased in these matters.
Nevertheless, I must say that NYC-based free form radio legends, WFMU, are incredibly over rated. Sure, they have a few shows that are quite progressive in their sound. And, yes, the majority of their remaining shows do not play a lot of material that you would hear on commercial stations. These shows do, however, tend to be focused on a lot of novelty crap, which, again, is outside of the mainstream, but that alone doesn't make it good music nor is it really the kind of boundary pushing programming that truly committted underground stations should be featuring. Overall, I'm sorry, but I'm not very impressed with WFMU.
If KFJC were in NYC, instead of Los Altos Hills, CA, we'd rightfully be reknown as being the most cutting edge station on the planet - and we'd be blowin' the doors off of WFMU!