So I found out about stdbuf. To get it:
# apt-get install coreutils
If you want your ssh client to use line-buffered streams use -t -t.
So I ended up with:
# su -c "stdbuf -oL ssh -t -t /usr/bin/tail -f /var/input.log | stdbuf -oL tr -c '\\11\\12\\15\\40-\\176" myuser \ | tee -a /tmp/input.log \ | grep --line-buffered -v "...ignore..." \ >> /tmp/output.log
Holy command-line Batman!