filter_alignment.py -i pynast_aligned/otus_aligned.fasta -o pynast_aligned/ -e 0.10 -g 0.80 #(assume -e will suppresss default GG lane mask)
Those settings should be fine (the settings will be different on versions of QIIME earlier than 1.9.0, if so, use a value -e 0.0005, due to changes in the order of filtering).
Since the script will be finding the most entropic/gapped positions, it will be fine for 16S as well as 18S or mixed 18S/16S alignments.