Aquaculture is accounting for more production volume globally, especially as in China. There is however an impression that aquaculture causes much more environmental pollution.
Aquaculture is not as environmentally friendly as many believe it to be but it depends on the type of aquaculture being practiced. For example milkfish and shrimp aquaculture in South-East Asia has a long history and has been responsible for conversion of coastal mangrove forest into ponds that caused serious environmental degradation of adjacent coastal systems. Development of large shrimp ponds has also resulted in discharge of large volumes of nutrient-rich effluents from the ponds that increased coastal productivity thus causing massive algal blooms (e.g., Noctiluca) detrimental to many coastal systems. However, polyculture of shrimp and milkfish in many Indonesia rice paddies has shown to be environmentally sound. I think polyculture is a way going forward in many areas and I have attached a paper that looks at it.
In temperate regions salmon cage culture has been documented to cause nutrient enrichment and increase the abundance of parasites that attack wild stocks. I have attached a few papers that you may find helpful. There is a lot of literature on this subject. If you don't have access to university library e-Journals try Google Scholar search.
Difficult question in some respects. Aquaculture can provide a much more stable and managed source of fish, shrimp etc., it does however have some well known environmental pollution problems. Fishing on the other hand ranges over a much wider scope of people and skill levels and ranges from purely artisanal fishing to more advanced commercial operations (netting etc.) If subsistence fishing was managed more sustainably its certainly as good as aquaculture ventures.
I agree that it is a difficult question that needs to be addressed, and I think it is being addressed in many areas. My personal interest is in aquaculture of species at the bottom of food chains that can be fed without degrading wild fish stocks that are at the base of marine food chains that ultimately support wild fisheries. Moving the coastal salmon pen aquaculture into land-based operations could address the pollution and parasite issues associated with the industry, and finding suitable food source other that so called marine trash-fish (which are needed b wild fish populations) would be a step in the right direction.