You should lower your credence in the specificity of hypotheses. When someone says that there is a theory about "rats," is it really the genus Rattus or the order Rodentia?

I don't know about the credibility of the Smithsonian, but most contrarian claims about the cause of the Black Death are complete nonsense and are invalidated by DNA evidence.

DNA establishes that the plague was caused by a particular bacterium that lives in fleas, mainly on rodents. The hypotheses that it was spread directly between humans or by human fleas are possible, but not popular. Almost everyone agrees that it was spread by fleas on rodents, but there is some disagreement about which rodents. It isn't even clear that there is a single rodent vector. For example, perhaps the fast spread was by rats on ships, but the spread inland was by native rodents.