My $0.02 worth...
If you could only do one glass bottom boat which would you do? This is our first trip to the Keys. We are staying in Key Largo 2 nights and Key West 2 nights. Not sure whether to do John Pennekamp's boat ($25) or the Fury ($42) in Key West. Does anyone know a better one to do? Our trip is early December.
I don't know about differences between the boats, but the
reef out off Pennekamp State Park is not to be missed (either by snorkeling or by glass bottom boat) if you are actually staying in Key Largo --- a place which frankly doesn't really have a whole let else going for it (at least IMnsHO) aside from a few good eating places.
If you have only two nights in Key West, I would not allocate
any of that limited time to a glass bottom boat excursion in KW, with so much else to see and do there.
Just my personal opinion, but based upon having spent more than a few weeks in both places over the years. We actually owned a timeshare week in Key Largo for a while (at Florida Bay Club) but didn't particularly like the place (or Key Largo) much. We also owned a week in Key West (at Coconut Mallory). Sold both some years ago, preferring to "pass" on Key Largo entirely in the future, just renting a week in Key West only occasionally --- at better timeshare facilities than Coconut Mallory.