Yeah, I would definitely recommend Port Douglas (Dougie) instead of Cairns. Dougie seems much more "small town" and laid back. We didn't spend much time in Cairns though, so others may have a different take. Dougie was closer to the Daintree NP and Mossman gorge as well which is a plus. There also seem to be a lot of condo-type accommodations there, which are nice as they are usually more comfortable and private.

As for the reef tours...most do seem fairly crowded. If you go to the outer reef it seems most have a semi-permanent platform. The boat takes you to the platform and you can do different activities from the platform (swimming, snorkeling, diving, helicopter rides, semi-sub rides). There is plenty of room on the platform, but they are pretty basic...ie metal benches/chairs without many good places to hang-out and relax. Quicksilver was the operator who we went with and they seem like a fairly big group. You may have better luck if you check into other operators. There should definitely be someone with a smaller boat doing tours to the reef. Local tour companies would likely be able to point you in the direction of a good small tour. Or just use google since we live in the age of the internet

Stephen