That's kind of expected over time in a stable two-party system; the periods of declining polarization are actually the periods just before partisan realignments, where the divides underlying old coalitions are losing salience, so the major parties are less coherent.

After WWII (or, really, FDR's first campaign) the party system entered a long realignment along what became the modern American left/right axis which was basically completed in the early 1990s. Which is why polarization increased throughout the post-WWII period, but also why it was turbocharged from the Clinton era on.