The ferry does run all through the year though if the river is very low there may be problems. Certainly the big boats which travel from Mopti to Tombouctou can only do the journey when the river is high but I've never known the ferry stop. The ferry (one boat is bigger than the other) is rather like a open sided, flat bottom landing craft which draws very little water. In November/December you'll have no problems as the river is still fairly high and the rains have been OK this year.
If you leave Tombouctou early (don't attempt the piste in the dark) you could get as far as Savare in a day where there is a pretty decent hotel called La Savana run by a fairly dotty French woman called Jacqui, otherwise it's Douentza then another overnight in Segou.
Hope this helps.