Most TOS novels take place after the TV series, since they were nearly all written after the series. The few exceptions usually have specific story reasons to take place between episodes and thus clearly state where they take place. (Well, usually clearly. There are a couple of older novels, Web of the Romulans and Double, Double, which purport to take place immediately after season 1 episodes -- respectively "Tomorrow is Yesterday" and "What Are Little Girls Made Of?" -- yet feature Chekov and reference events from season 3.)
With TNG, DS9, or VGR novels, you can usually tell by the stardate, if one is given, and the books from the past 2-3 decades usually have "Historian's Notes" specifying when they take place.