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!