Port Douglas is about an hour drive north of Cairns and has a couple of good day boats like
Poseidon and Silversonic. Both take around 80 passengers.
There is Quicksilvers' pontoon, but its a big boat that goes out to a stable pontoon which offers glass bottom boats, etc. Not sure if your wife would like something like this or not.
Port is a much quieter town than Cairns which is the central hub for trips to the GBR and hence a lot more choices.
Pretty much all the trips have 60+ passengers to make it economical. These trips are fast and go to the Outer Reef with has some of the better diving out of Cairns for day trips.
I think if you want a small quieter boat then it sounds like
Reef Day Tripper (27 passengers) would suit as its still visits some good sites.
One of the best day trips would be
Tusa and although it does take around 60-80 passengers it offers the most time at the Reef, great service and some really great sites suitable for both snorkel and dive.
For me in the FNQ look at Tusa or Day Tripper.
Mission Beach has very little to offer nowadays (diving wise - its still a stunning place to visit and highly recommended for beaches and quiet get away). Since a cyclone caused a lot of damage to the area including Dunk Island (which is still closed for overnight stays) a few years ago, there are no real reef trips there.
Magnetic island itself has a lot to offer for a getaway but not so much diving either. Not great diving off of the beach (very low vis) so you would need to take a day boat out of there, but the diving is far better in Cairns or down south (Noosa etc).
I wil let some others who dive more out of the Sunshine coast with better reports (I am based in Cairns now, but owned a dive business in Mission beach for years and also run courses for other dive shops in Noosa, so know a fair bit about these areas).
WetPup is a regular contributor here and is based in Townsville so am sure will give a far better run down of Townsville and Magnetic Island.