NuGet is designed to allow you to easily add code libraries to your project. Things like JSON.NET, Entity Framework, etc.
Chocolatey is actually built on top of the NuGet package system, but it is designed to fill a different need. Chocolatey wraps up applications and other executables and makes it easy to install them on your computer. For example, tools like Git, Notepad++, etc. can be easily installed with a command like cinst git.
If you have an open source project which is a library that is to be used in other developers' projects, then you should submit it to NuGet.
If it is an application that users would normally install, then create a Chocolatey package that users can easily install and update from the command line.
