What are the best ways to find cheap, but clean hotels?

My friend and I are traveling to NJ and NYC. (Too bad we don’t know anyone that lives in the area!) So I’m wondering.. where are the best sites to find cheap AND CLEAN places to stay? I’m guessing that’s going to be the thing we spend the most amount of money on. Just the reg.. like orbitz.com, expedia, etc.? Or do you know of any awesome sites? ThankS!!!