If they're fairly tame, and won't be too stressed out by not being able to dig, you can't beat the "reptile carpet" type materials. They are easy to clean, and won't usually create a harborage for fruit flies or fungus gnats in your house. If you go this route, place a lot of structure in the enclosure for them to hide under and around. Also, make them a nice hide box. Newspaper is a lower cost, but less attractive and more wasteful alternative to this.
If the turtles are a little more skittish, and would require digging to feel secure...I'd go with organice potting soil/top soil with an equal volume of well dried leaves. Mix the two together, and then you can add an additional pile of leaves at one end of the enclosure for hiding. Purchase organic soil, free of any additives; chemicals, perlite, vermiculite, water absorbing materials, etc. I wouldn't use soil from the yard, unless you don't mind importing the bugs that invariably come along with it.
I'd stay away from the "wetter" materials like sphagnum moss and peat moss due to Three-toes' propensity towards getting shell infections.
Good luck keeping them indoors for the winter. While I believe that outside is best for the turtle, having them in can be a real "bonding experience" for the keeper. Just remember the importance of UVA/UVB basking for health and happiness. A 75 watt Powersun bulb from Zoomed, set at the proper height, would be ideal for an adult Three-toed box turtle.
I'd love to see pictures of your turtles.