The dock use the default file manager of the desktop environment.
In your file manager, right click on a folder, open the properties, and try to change the application used to open the folder.
The other method is to edit the config files, which seem to be in
According to the Ubuntu Default File Manager page
, the file seem to be
In have more files in the directory, so I think you'd better check before that you don't have already defined something:
grep directory ~/.local/share/applications/*
You will have to edit those lines (use the program you want instead of thunar):