I used to grow a lot bananas in the yard, and I would just chop off the sucker with a shovel and replant it... never had a problem. They are pretty hardy plants. If this is a potted plant, you could probably just dump the entire rootball out of the pot and carefully cut away the suckers you want to remove. When growing bananas for fruit, you always want to leave 2-3 suckers on so that once the main plant dies (after fruiting) you have at least 2 backups growing on the way so you don't have to wait too long for the next set of bananas.

At 6" tall the pups may be to small to remove,you can try it if you not worried about losing one.

I would wait until the spring and then just take a sharp shovel and dig it up that way. Plant it in a pot and keep it well watered and in a month you can put it in a bigger pot, or in the ground for the summer.
Good luck!
-Alex