Apple - "System" storage on macOS Sierra is 470GB!
Download OmniDiskSweeper and analyze your hard drive.
OmniDiskSweeper will show you the files on your drive, in descending order by size, and letting you decide what to do with them. Delete away, but exercise caution.
OmniDiskSweeper will show detail of space usage: Select System and start cleaning.
It could be the Time Machine backup file that takes almost all the free space.
I fixed it on mine, it was to do with the BELLMIN' Time Machine Queue Backup files (i.e. files that meant to go onto the Time Machine but haven't been moved yet due to the TM not reachable or away from home etc).
Do the following (no need to buy or download any additional tools):
Go to Terminal
List all TM objects by doing the following
sudo tmutil listlocalsnapshots /It will come back with few items:
com.apple.TimeMachine.2018-04-01-122047 com.apple.TimeMachine.2018-04-01-183626Remove these by doing:
sudo tmutil deletelocalsnapshots 2018-04-01-122047 sudo tmutil deletelocalsnapshots 2018-04-01-183626
Where the date is taken from the output from step-3 above.
Leave it for a while to catch it's breath. You can check the disk space by executing the df -m command and notice the % of your Free Space, doing more df -m every few seconds will show an increase, once done it would stabilise.
Your system may need to reindex the file system to correctly show disk usage amounts. Indexing is handled by Spotlight. Using system preferences>spotlight, add your drive to the list of folders not to index for privacy reasons. Reboot and then remove that entry. Your computer will be slow during the reindex process, but after it should show the appropriate amounts.
As for figuring out where your disk is being weighed down, I like to use Grand Perspective. http://grandperspectiv.sourceforge.net/ It gives a visual graph of the files you have and how large they are.