The difference is that a patent is a federal document proving ownership of an idea, and an NDA is simply a contract between two people. So in other words NDA’s only recognize the signatures on the contract, whereas patents provide proof that you own the idea entirely. So, if you sign an idea with a coworker, and develop this product, but then the coworker tells his other friend about it who also decides to build the similar product, you would not be able to sue the coworkers friend because there is no paper trail between you and the friend. In the court of law, a patent certainly holds more weight than an NDA.

http://wwwfloridaipblog.com/archives/patents-vs-non-disclosure-agreements-what-gives-you-more-protection/