We did.
It was OK. Not a bad way to spend a few hours on the ocean with little kids. You should know that the "glass bottom" is something you need to stand around, my five year old was tall enough to see (he is fairly tall for his age) but the four year old we needed to lift up. If the weather is choppy you won't see the shipwreck - which is a WWII boat that they blew up - big flat peices of steel lying on the bottom - nothing "shipwrecky" to a little boy (though he did think it was cool, just didn't meet his expectations of "shipwreck.") They spend some time driving through the harbor and looking at the estates (Tiger Woods, Oprah), which didn't interest the kids, but did interest some of the adults. They sold drinks and snacks on board, but I'd recommend you bring your own.