You can add the ST3/Python3 branch (where available) to Package Control via the `Add Repository` command and then install. Repositories take precedence over packages in Package Control's library.
For example, to install the ST3 version of FuzzyFileNav add the following branch: https://github.com/facelessuser/FuzzyFileNav/tree/ST3
And then install via the `Install Package` command.
Notes: not all packages have working ports or at all. Remove the ST2 package first, if you've installed it by mistake.
Hope this helps,