One more option to consider: We recently released a method - decontam - that identifies contaminants based on two statistical signatures: higher frequency in low concentration samples and higher prevalence in negative controls. You can read more details in the preprint: Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.
Right now decontam is available as an R package. In the future we intend to make decontam available through the q2-quality-control plugin, but I can't give you a timeline on that yet.