IMHO the best option is to use a tool like Clonezilla.
I suggest you to get a copy of Parted Magic (which contains a lot of useful tools for disk and system maintenance, including Clonezilla), and run it as a LiveCD (or LiveUSB).
Clonezilla itself has a simple user interface that helps you to properly set the options you need, but if you spend a little time to learn the variables, it can also be launched from the command line.
When working with partitions, it is always better to have them unmounted, something that you can't always do if you are logged in in your system and want to work with the disk where the OS in installed.