No, technically the use of "one" is incorrect, yet such a phrase is common in most American English speech.
As you said, the subject of the sentence is plural, and the verb "are", reflects this (as apposed to "is"). This makes the singular word "one" completely out of the question.
If we add the word "of" - to make "one of" - then you got yourself a sentence (I am reasonably sure you just erroneously forgot the "of", but I figured its still a good point to make). Consider the phrase "one of" as a synonym for "among". This way, your sentence reads: "Honda and Toyate are among the best selling cars in the US"
I hope this clarifies this particular usage.
As for the superlative nature, typically in English the meaning of superlative is slightly augmented by the use of determiners. If you use an indefinite article as the determiner ("a" or "an"), you get what you were describing as "somewhere on top but not necessarily the very top"; a relevant example would be: "Honda and Toyota are a top-selling cars". But, to produce the "very top" you use the definite article "the", as in: "Honda and Toyota are the top selling cars". (also notice the use of indefinite vs. definite articles in this paragraph, if you are unsure on that lol).