Snag,
Are you talking about the Toronto Humber Yacht club up the Humber river or the ones in Humber Bay? Mimico or the Etobicoke Yacht Club? I know a little bit about the Toronto waterfront and at first glance my reply would be you would definately be allowed to fish where there are navigatble waters, however like some have said there are certain exceptions but I have never heard of any for the waterfront except in the Toronto Harbour boundries which are controlled by the Toronto Port Authority which would be similar to what snowball is referring to in Thunder Bay because it is a commercial Port run by a federal Agency and they have exclusive rights over the waterways in the port.
I can try and find out more but if it was me I would just politely say call the Police, They will come and sort it out for you. If your in the wrong which I doubt you are you will most likely be just asked to leave. Some Marina types think they own everything around them including the water but they are in most cases wrong. If they have any rights at all to the area they will have to produce proof to the officers.
Also a quick call to the MNR for the Toronto area should clear that up for you. If your lawfully fishing they cannot harass you remember.
Craig