Salmon do something that makes managing them relatively easy—they return to spawn in the place where they were born. This means that fisheries managers can, year in and year out, determine how many salmon there are and how many we can take without damaging the long term viability of a given population. True, there are places like far eastern Russia where not-so-careful salmon census-taking occurs, but the majority of canned salmon comes to our supermarkets from Alaska, where careful monitoring is in place and to which the Marine Stewardship Council has issued sustainability certification.
Tuna range far and wide across the oceans. Estimates of tuna population sizes are therefore considerably less exact than those for salmon. In addition, tuna stocks are fished by multiple nations simultaneously, with a significant amount of tuna coming from the no man's land of the High Seas. The management that does exist is centered around politically charged bodies called Regional Fisheries Management Organizations (RFMOs). Catch data provided to these RFMOs from the dozens of nations that fish tuna can be imprecise and hard to obtain. All of this begs the question—if we can't really estimate how many tuna there are and how many tuna are being caught, how can we really know if we are managing them correctly?
2. We know how to catch salmon without significantly hurting the marine environment.
It has taken a while, but we have figured out how to catch salmon in a responsible way that does not do too much harm to other creatures. In the bad old days, canneries would sometimes string nets across the entire width of a river, killing everything that migrated inland. But now salmon fishing is much more selective. Salmon used for canning is generally caught with gear that obstructs only a small portion of salmons' natal rivers. Mesh sizes of nets can be altered on a daily basis to select the particular fish that is coming into the river, allowing other fish to pass through unharmed. Marine mammals do occasionally get ensnared in salmon nets, but the bycatch is nowhere near as bad as it is for tuna fishing, in which longlines hundreds of miles long can catch threatened sea turtles and sharks.
Tuna purse seiners encircle entire schools of tuna and often trap dolphin in the process. Add to that the frequent use of FADs, or Floating Aggregating Devices, in developing nations—which draw tuna in from far and wide, skewing the amount of tuna a fisherman would normally be able to track down—and you have a major problem with the way tuna are caught worldwide.
3. The species of salmon used in canned salmon eat lower on the food chain than tuna, and are thus lower in toxins.
Although the sorts of tuna used for canning are not giant predators like Atlantic bluefin or bigeye, they are still "alpha" predators, consuming fish that have in turn consumed other fish or crustaceans further down the food chain. Skipjack, albacore, and the other "canning" tunas can thus become storehouses for toxins like mercury and other heavy metals when these substances "bio-accumulate" from one food-chain level to the next. Pinks, chums, and sockeyes, in contrast—the salmon most commonly used for canning—feed mostly on small crustaceans and even near-microscopic plankton. Their pinkish-orange flesh is in fact a direct result of the pigments from these crustaceans. These salmon are as high if not higher in omega-3 fatty acids as tuna and bear none of the toxic risks of tuna.