I have a feeling the answer has more to do with the history of the two countries than with any linguistic reason, so that's why I'm posting my question here instead of Asklinguistics.
As far as I know, both are just as incomprehensible to a standard German speaker and both are spoken in different countries, so why did the Dutch decide to call their dialect a separate language, but the Swiss didn't?
I am afraid the reason is linguistic. According to Pijnenburg (pdf in dutch, the second chapter) the reason why Dutch diverted from German is twofold, the high German consonant shift didn't happen in dutch and the dutch dialectcontinuum was influenced by oldfrankish. High german did follow the consonant shift and low german was influenced by oldsaxon, not oldfrankish. For knowledgeable comments I advise you to post this question in /r/asklinguistics.
Of course history does have something to do with how the languageborders are determined, an interesting remark by Pijnenburg was the influence the administration of the bishopric of Utrecht had on the language of especially the current province of Overijssel, since Utrecht (in the frankish dialectcontinuum) ruled that area, then called Oversticht. Utrecht's civil servants wrote in middledutch, while the area was part of the lowergerman dialectcontinuum. The local Overijssel dialects are still called nedersaksisch, lowersaxon.