I have one piece of LR rubble with a little red bubble algae on it (three bubbles' worth). It has a mushroom on it that I don't want to hurt.

I can take the rock out easily to work on it in a bowl of water.

Is it pretty reliable to manually remove it, or should I break off the end that has in on there? I can do that without getting near the 'shroom.

Pluck them off, scrub the area with a toothbrush and then rinse it off. You should be fine