When I deploy my application in VS2010, I see two options: InstallShield LE and Visual Studio Installer. Why are there two options? What is the advantage of using InstallShield LE over Visual Studio Installer?

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These are just default tools that can help you create simple installers for your applications. Most difference are UI related, there’s not much functionality in either of them.
If you want to choose a setup authoring tool, take a look at these threads:
There are lots of threads like this which mention free and commercial setup authoring tools.
Basically, if you want a simple installer, you can use Visual Studio setup or InstallShield LE. If you want more advanced features, you need to find a different setup authoring tool that fits your needs.