You can change the order GMPC queries the metadata plugins in the config file (~/.gmpc/gmpc.cfg) By setting the priority config entry. The lower the value, the higher the query priority.
For example if you want to query the last.fm plugin before coveramazon plugin, change it priority value to a lower value then coveramazon.
[cover-amazon] priority="80" [cover-lastfm] priority="50"
In 0.17.0-beta1 there is a gui for this.