Native Americans never practiced "science" as we understand it. Would contemporary historians refer to Native Americans as living in a "dark age"? I highly doubt it, as this would suggest an air of European superiority.
"Dark" refers to a the idea held by Italians in the Renaissance that they were the darnedest smartest people to hang out with since the end of the Roman Empire and is a bit of a misconception, which is why we don't reapply it on other stuff. The only other place I know of where the phrase is used is in the name of the the "Greek Dark Age" after the Bronze Age Collapse, where the phrase refers to the lack of written records during the period. The topic has already been covered extensively in the linked questions and in others, although I'm sure there's room to add to the topic, as well as some "Dark Ages" I haven't heard of.