PaugusBayFireFighter posted a picture of what makes these waves in this thread a little while back.
https://www.winnipesaukee.com/forums...ess#post256595
On a more serious note , I often fish very early in the day and very often get on the water before the sun comes up and the lake is flat. You get to see a lot of things that you generally don't see after the wind and breeze comes up and ripples the water. If I had to guess you might have seen a beaver swimming or an otter. They generally swim very silently with there heads only just above a water leaving a wake that appears to be coming out of nowhere then stops and starts again.
Once in a while you get to see deer crossing but that you more than likely would have been able to identify.