Right, those are kind of in the same semantic cloud, but there are important differences.
Regarding hypotheses, an alternative hypothesis is just a different way of explaining a set of observations. My hypothesis is that the restaurant is closed because it is a holiday, yours is because they are out of business. In this class we will speak of auxiliary hypotheses, and these are hypotheses we adopt, often without evidence, for the purpose of maintaining the current hypothesis in the face of evidence against it. Ptolemy's epicycles were constructed as auxiliary hypotheses in this sense. If I tell you that it's unlikely they are out of business because they were open yesterday, you might adopt the auxiliary hypothesis that the owner died..
The word 'counterexample' is used in a lot of different ways in ordinary English, but in philosophy and logic it doesn't have anything especially to do with explanatory contexts. A counterexample to an argument is an imagined state of affairs in which the premises hold true, but the conclusion is false. If someone argues: Poodles are dogs, Fifi is a dog, so Fifi is a poodle, we would say this is invalid, because counterexamples exist. It could, e.g, be that Fifi is a labrador, since this is consistent with the truth of the premises.