Craigslist.org is a top 5 site on the Internet in my opinion. you can find anything here in under a minute and all for free and without logging in. Everything is simple and makes sense. I have found 4 different places to live on Craigslist all with no fee.
http://newyork.craigslist.org/hhh/

Property Guys is a Canadian sell-it-yourself site. I listed my house in Prince George with them when we were moving to Vancouver, and it worked out well. We had a decent number of people get in touch because of the listing.
http://www.propertyguys.com

As good a resource as any in the NYC area!

This is a quality secondary resource for online apartment finding.
http://www.apartments.com

This site is great for finding listings for any home purchase.
http://www.realtor.com/

This is a great place to look for a more expensive dwelling. Great, serious listings here. Very pricey to list a place for rent too. But worth it!
http://www.nytimes.com/pages/realestate/index.html

I tried this and it worked out pretty well. Its a very tough market out there, this site lets you keep all the money if you sell.
http://www.forsalebyowner.com

Great resource to find apartments for free.
http://www.rent.com

I just realized these 2 joined forces. Powerhouse for NY and the surrounding area of real estate in general.
http://villagevoice.trulia.com/NY/New_York/