I know this gets old but....

Subject: Backpages

http://newyork.backpage.com/online/classifieds/index

This is a decent website that you might want to try, I've been using it through out my apt search. But I must admit, I've had my major doubts on craigslist but to my surprise I just found a place using it. The best thing to do is know the area you want to live in and only search for by owner/ no fee apt's if that's all you can afford. The broker experience is no fun ride but leave it as your last option. I would also suggest checking these websites every day. I caught mine on craigslist on what seemed to be a whim, but i checked every day and all of a sudden I found one. Also try to track down brooklyn newspapers. I tried this one:
http://www.yournabe.com/classifieds/real_estate/for_rent/
www.HowToRentInNYC.com
This one is awesome- It's the only website I've found that lists owners and development companies direct. You may have to make a bunch of calls and ask if they have anything available but this is one of the only ways to override the brokers fee (if you don't find it on craigslist)
Hope that's helpful- first time in my life I had an answer to this question...Good luck!!