If you're looking to rent directly from a management comapny, bypassing a broker, I have found this site useful:
How To Rent In NYC .com- Rental advice and no-fee rental deals for renters in NYC - HOME click on "Management Companies & Landlords." Some on the list have a link to their website and you can do an apartment search. Since they are not brokers, they list actual apartments they have available and the actual prices.
Apartments in New York from Urban Sherpa does the same thing without having to go to each individual managment company website. However, it probably won't be as complete and up-to-the-minute as a managment company's own website.
If you want to go through a broker, I guess Craigslist is as good a place to start as any, and Craigslist has for rent by owner listings as well. Using a broker in this economic downturn may not be such a bad deal, as I've heard there are some managment companies/landlords who will pay the broker's fee. But if you go directly through the management company, you may be able to get a month's free rent instead. OTOH a broker may be able to have access to apartments that you won't find listed on the managment company/landlord websites.
As to Craigslist listings being fishy, I can tell you that one broker is still using on his webpage pictures from an old apartment of mine as a current listing, even though said apartment no longer exists as the building was gut renovated and converted to condominiums. But to be fair, apartments move so fast here (well, a little slower these days) that it is simply not possible for a broker to photograph every rental apartment as it becomes available, and also have time to show apartments, do paperwork, etc. (A management company can because they have a set number of buildings).
Good Luck!