Usually, a proof by contradiction of the statement $p \implies q$ is when you assume that the opposite of the desired conclusion is true (i.e., assume the negation of $q$ is true), and follow a few logical implications until you reach a statement that somehow explicitly or implicitly contradicts an initial assumption from the statement $p$.
Meanwhile, a counterexample of the same statement $p \implies q$ is when you say, "Hold on! This statement can't be true, because here is an example where $p$ holds, but $q$ does not."
In proof by contradiction of the statement $p \implies q$, at the end of the day you actually are proving that $p$ implies $q$. But if you find a counterexample for the statement $p \implies q$, then you are actually disproving the claim $p \implies q$, so applying proof by contradiction to a statement does the opposite of applying proof by counterexample.