The correct way to lock down external access to MySQL is with the bind-address directive in /etc/mysql.cnf, as described by daisy. You can't usefully stop someone with a valid MySQL account from logging in locally (but note that a UNIX account does not imply a MySQL account; they are distinct from each other).
I'm going to answer the other part of your question:
I assume I should lock some extra ports besides 3306. Is that correct?
# Allow incoming TCP ports TCP_IN = "20,21,22,25,53,80,110,143,443,465,587,993,995,9000"
At the moment your csf.conf file sets your firewall to allow in so many services it's hardly worth using.
- 20 - FTP data (why are you allowing FTP over the Internet at all?)
- 21 - FTP command (ditto)
- 22 - SSH (this is good but ensure your accounts are locked down tight; consider disabling all non-certificate logins)
- 25 - SMTP inbound (are you really running an incoming mail server?)
- 53 - DNS (are you really running public DNS?)
- 80 - HTTP (are you running a web server?)
- 110 - POP3 (obsolete protocol; if you are running a mail server consider IMAPS on 993 instead)
- 143 - IMAP (insecure; use IMAPS on 993 instead)
- 443 - HTTPS (are you running a web server?)
- 465 - SMTPS (are you really running a public mail server?)
- 587 - SMTP-MSA (ditto)
- 993 - IMAPS (only if you are receiving mail messages on this server for reading)
- 995 POP3S (secure but still obsolete)
- 9000 - who knows
If you don't offer a service then don't allow it in. POP3, IMAP and POP3S should all be switched off in favour of IMAPS (if at all). Don't offer SMTP* unless you really are running a mail server that needs to receive emails from the Internet. Don't run FTP. Use SSH for file transfer instead.
If you want to use MySQL Workbench on a different system you can still have MySQL set to permit only local connections by running a forwarder across ssh. I do this for a couple of my servers:
ssh -nf -L localhost:3306:localhost:3306 ADDRESS_OF_REMOTE_SYSTEM sleep 60
# Using Workbench, now connect to MySQL seemingly on the local machine