How can I find what is using the rest of my drive? I am using a Macbook air.  64GB.

My user directory has used 20.47GB

Disk Utility shows 'Other' is 41.33GB and I only have 2.9GB free.

What tools or command line commands can I use to find out what is taking up large amounts of this.

I can use finder with all files and sort by size but that is already about my directory and the space taken seems outside of my directory.
I use Daisy Disk to keep tabs on what's using up space on my disks. Like @Hoshts and @Joonas have mentioned in their comments on another answer it's not free, but gorgeous and easy to understand. Money well spent, in my opinion, unless you're just looking for a one-time solution.

One thing to keep in mind - the Mac App Store version of Daisy Disk is sandboxed - which means only the files your user can read will be counted.

If you use the direct download version of the app (which will assume the license from the MAS version if you install both and run the direct version after launching the MAS version one time and quitting it.) - it can run as Administrator and show all the files for all users on your Mac.