This problem has been plaguing me for quite some time and I finally figured out a way to remedy it

1. Backup your phone with Blackberry Desktop Manager
2. Create a new, empty gmail account (ie elitastecontacts@gmail.com)
3. Download google sync and sync with your new empty gmail account
4. Go to Contacts>More>Find and Merge Duplicates. You might have to do this a handful of times. In my experience it found and merged about 300-700 contacts at a time so depending on how many contacts you have (with all my duplicates, I had 21,000) it might take a minute.
5. Export to .CSV file
6. Sign out of empty gmail account and into your normal gmail account
7. Import the CSV file you downloaded
8. Go to More>Find and Merge Duplicates. Again, you might have to do this a handful of times
9. Sign out of google sync on your phone
10. Plug your phone back into the computer. Again, make sure you have your phone backed up.
11. Clear the contacts on your phone
12. Your phone should now be empty of contacts
13. Sign into google sync using your normal gmail account.
14. Go to sync contacts (this might take a while, make sure you’re connected to wifi, it will be easier)
15. All the contacts that you Find and Merged duplicates of on gmail should now be on your phone. You might have a few stragglers. Go into your gmail contacts, delete the remaining duplicates by hand and then resync. You should now be duplicate free.

Do not use Contact Cleaner or anything else. Google’s “Find and Merge Duplicates” is the smartest one out there