On a couple of Magento1 sites I've had to configure nginx and have found .user.ini files to be most reliable. It is significantly easier than editing the system php.ini then restarting PHP-FPM and worrying about automatic updates over writing your work. Although the exact filename can be changed with user_ini.filename setting I have yet to see any server change this.
For Magento 2 I suggest two files, /.user.ini and /pub/.user.ini, to allow for situations where Magento files are not stored in the web root and are linked to instead. Their content is derived from the .htaccess.