We had an overnight in Cairns a bit over a year ago, stayed at the Shangri La Marina. VERY nice. They were mid-upgrade then (some rooms not yet complete), I knew it and asked for a room on the updated floor.

We departed the next day for the reef. On our return we rented a 4x4 and drove CNS-(via tablelands) Cooktown- (viaBloomfield track)-Mossman. Spend 4 days there, then flew down to SYD and back. Very much enjoyed the tablelands, as well as Daintree/Cape Trib. Didnt spend much time at all in Cairns. Not sure what else you are doing elsewhere, but snorkling something out on the reef would be a must do IMO.