De Boeck is the main company for guided coach tours in and around Brussels, and they have a trip to Cologne and the Rhine (see list on the left) brussels-city-tours.com/engels/engframes.htm
However, I took 2 tours with them more than 20 years ago and thought they were appalling, plus if you look at the discussion on hop-on, hop-off buses, it is now De Boeck that runs the blue and red ones and it appears they have not bothered to update the commentary from when they took the blue ones over from STIB (Brussels city transport company) about 5 years ago. So, I can't claim that this is a "good, reputable tour operator", but it's the best you are likely to find.
An alternative might be to simply take the train to Aachen and Cologne and find out in advance what the local tourist office can offer you. These days it is often possible to rent audio-guides for a do-it-yourself guided tour, and in Cologne at least the station could not be more central - it's right next to the cathedral.