Hey MrScotch... So I dive both of these areas regularly. I am clearly biased towards Tobermory, but let me give you my best unbiased opinion...
Thousand Islands
* warm water.. wetsuit in July might do it
* some nice wrecks, from old schooners to modern lakers (tech depths - Jodrey)
* strong currents
* a couple of charter operators (I recommend Thousand Island Pleasure Diving - Wayne Green)
- summer water is murky and a bit stinky
- massive zebra mussel issues
- border crossings as some wrecks are one one side, some on the other
Tobermory
* gorgeous clear water
* nice wrecks - mainly older sailing vessels, plus purpose sunk Niagara
* beautiful topside scenery
* light zebra mussel coverage
* nice beaches and perfect water on the Huron side
- one dive operator as of today, but capacity remains the same (Divers Den - Kelly)
- cold water... dry suit for sure for deeper wrecks
Topside... well different.. Thousand islands is a busy area... boat traffic, but lots of options for eating etc. While the village of Tobermory itself gets busy, it's located at the end of the Bruce Peninsula which is a UNEXSO Heritage Site, so lots of hiking options etc.
Accommodation may be an issue in July in Tobermory, so I wouldn't leave it too late to book. (If you are a smaller group, my place is for rent potentially). Tobermory has a couple of nice pubs and some decent restaurants.
Both areas have their charm, but I find the diving way better in Tobermory. If you look at my website (see below) there are tons of pics from he area)
By all means, hit me up if you need any more information~