On the one hand, the boulder has always seemed fishy to me. It's a remote location and I doubt many people would track something that small, or care enough about it to know about the seasonal changes at that boulder. It also doesn't make a lot of sense to me geologically, although it's possible. I also years ago remember people familiar with the site jokingly talking about how "if there were a boulder there..." which lent the whole thing a sense of fiction when I started reading about it. It was easy to see how a humorous fantasy could change into folk legend and then into documentation.
On the other hand, where are the photos? Where's the meticulous documentation? To trek all the way there to address this and then not take copious photos to share with the media?
They also got lost, which adds to my skepticism they even made it there, or were sure they did. Can you get lost there? I suppose -- there are a ton of islands and things there so I can see that -- but the area is blanketed with topo map coverage, and you've got GPS now. If someone were to get lost there, I'd question whether or not they even got to where they wanted to begin with. Siskiwit Lake is a fairly large feature on Isle Royale, and the nesting doll nature of the goal makes your target hard to miss.
In short, I wouldn't be surprised if the boulder isn't there (or isn't surrounded by water). However, I also wouldn't be surprised if this guy and his mother never actually went to where they claimed to go.