Use the command line tool mdutil.
For example, say you connect an HFS+ journaled volume named "LEAVE_ME_BE"
Use the following command to disable indexing of the volume. If ownership is enabled, running as sudo
may be necessary:
sudo mdutil -i off /Volumes/LEAVE_ME_BE
Check indexing status of all connected volumes:
mdutil -s /Volumes/*
Read the man page linked above for further options (disabling spotlight for the volume all together, etc.)