I have an application where I need to store 3rd party credentials to services like Amazon S3, FTP, SFTP, etc..
I know that it is possible to access some of those sys
You need to investigate the use of keystores. TruCrypt is an example of such a keystore, but this is a personal keystore, not intended for service level credentials.
You won't be able to avoid storing their passwords in a format that someone can get access to, the goal is to minimize who can access the information. Putting in the same MySQL as application data is asking for disaster.