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I know all of these places well and have visited them all many times as I lived in the area for several years. Freiburg is one of my favourite German cities--with a beautiful Gothic Cathedral and town centre that was faithfully rebuilt after the war. Breisach is OK, but nothing special and that stretch of the Rhine where it is located is not very picturesque at all.
I would opt for the Colmar and Riquewihr tour. Colmar is a beautiful large town/small city with a centre filled with half-timbered buildings and Renaissance architecture, criss-crossed by very scenic canals. Riquewihr is a picture-perfect walled wine village with many buildings from the 16th Century. It is home to some of the top Alsatian wine producers including Doppf & Irion, and a good place to buy a bottle or two (as is Colmar).
The only downside to Riquewihr is that in tourist season it can be a bit overwhelming with so many bus tours crowding into town (yours included). A bonus is that you will be travelling on part of the Route du Vin which is picturesque, unlike the road from Breisach to Freiburg (the best scenery in that direction is eastward from Freiburg into the Black Forest hills.)
Either tour will be very interesting, but I do think that the Alsatian tour is the one to choose.