Look at a chart and make note of choke points between ports (marinas and public docks). Traffic will be heaviest on a straight line between these choke points. A classic example is the triangular section of lake between Governor's, Stonedam, Bear, Mark, and Timber Islands, and Meredith Neck. That spot sits between most of the popular ports and marinas and is loaded with choke points. At it's worst, it's not really that bad though, compared to other places I have been been.
That said, in many cases, the coves and such that are off the beaten path and protected will also have lots of wake action because people seek out calm water for water sports (and then make giant wakes in them...).
Your best bet is to simply have a plan for waves, either man-made or from wind and not worry about it. There are tons of products on the market to protect a docked boat from waves. A mooring is also a great way to make waves irrelevant to a boat.
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