Hi... Suggestion - move it into a larger pot (but try for wider than deeper to encourage lateral growth for its eventual bonsai pot). A larger pot now will help it grow faster, but when you repot just crumble off most of the soil, gently move roots more horizontally, but don't cut any now, and be very careful about breaking any off. For soil, add a lot of grit and less potting soil. However, IF you have an outdoor place that's relatively protected from wind and bad drainage, forget repotting and just plant it, but mulch very well all around and above (though not right up the trunk or you could have rot problems. You just have time to acclimate to being out and colder nights. Don't worry about 'bonsai' soil of course, though try to not have it in a veggie or flower bed of black loamy stuff that just compacts and holds too much water. OR you could dig a pit for the new larger pot (above the spring water table level if you can find out where it is), with mulch inside and around it, and cover from a well slanted wooden flip up, that you would open when it gets sunny in the spring. It won't really need light over the winter with no leaves, and putting snow on it helps to insulate, but in late Feb. it will need light to bud properly. Just don't take it out til the last frost has passed (May 1?).

To answer your question, Ginkgo are wonderfully adaptable to bonsai culture.

Should I remove one of these stems?
If so, when? Now? In the Spring?

I've seen some gingko bonsai with several stems but, knowing nothing about bonsai, I wonder if that might be too much of a challenge.

More energy (theoretically) will go into one trunk if others are removed (it's only a 'stem' if it's still green and soft), but it's up to you. An uneven number is always better than an even number though (and you seem to have 3).