.config directory is a newish development courtesy of XDG that seems, deservedly, to have won favour.
Personally, I don't mind a dot directory of your own. A bunch of separate dot files (ala bash and various old school tools) in the toplevel of $HOME is a bit silly. Choosing a single dot file is a bad idea, because if in the future you realize maybe there are a couple more files that would be good to have, you have a possible backward compatibility issue, etc. So don't bother starting out that way. Use a directory, even if you are only going to have one file in it.
A better place for that directory is still in
~/.config, unless you are very lazy, because of course you must first check to make sure it actually exists and create it if necessary (which is fine). Note you don't need a dot prefix if your directory is in the .config directory.
So to summarize:
- use a directory, not a standalone file
- put that directory in