Canal Tour Advice

I'll only answer for Belgium. In Bruges, you can see everything you see from the boat while walking around.

In Rotterdam it's not so much canals in my experience, it's the Maas River. There I think a river and docks tour is worth it. I would also suggest going to see the old SS Rotterdam at it's now permanent berth.
She has her own water taxi berth.
I also suggest taking the waterbus from Rotterdam to Dordrecht, coming back by train. The obvious stop off point of course on the water bus is Kinderdijk for the windmills.

Over the years I have done canal tours in Bruges, Ghent, Haarlem and Amsterdam. I would say Amsterdam is best mostly because there are more miles of canals there. Bruges was good but as mentioned you see most of the sights as you are walking around. Haarlem was pretty good too and got me to a windmill I did not see on foot. Ghent (which I know you didn't mention but someone might do a search in the future) was the least interesting as when I went there were a couple of out and back segments instead of a loop.

We did the canal tours in both Bruges and Amsterdam and LOVED both. However, if you can only do one canal tour, do Amsterdam, simply because it's much bigger, as others have noted.

Thanks everyone for your input. We will definitely do the canal tour in Amsterdam. Perhaps in another city as well if the weather and timing are right.