The second one which is 'hover over a link' is correct. The meaning to the word hover is to hang fluttering or suspended in the air, to keep lingering about; wait near at hand, to remain in an uncertain or irresolute state; waver.n

In the context you mentioned, the cursor is imagined to be moving above and over the hyperlink. Hence, hover over is the right choice. Similarly, hovering over its prey is right because of the same reason.