trying to decide between the glass-bottom boat trip at Pennekamp SP, and the one at Biscayne NP for end of Jan trip to the Keys - which one would have better viewing this time of year?

I haven't taken a trip out of Biscayne NP but have done many snorkel trips out of Pennekamp. Given the location of the two, I suspect that Pennekamp would be the better choice.
If you are staying in the Keys (vs. staying on the Mainland), then I would absolutely pick Pennekamp. There would be no reason to add the extra drive time to Biscayne NP.

Am I correct that at that time of year one would need to do the boat? I.e. water not warm enough for "immersion"? In fact, even assuming the water is warm enough (which I doubt), is it correct that the reefs are not close to shore? I.e. that one has to take some sort of boat out to snorkel anyway? Thanks.

Yes, even to snorkel a boat is required, because of distance, not temperature. You might be surprised at how swimmable the water is in the keys in January. I've done the Pennekamp snorkeling trip, by the way, and its great. I live in Florida, and I have never known anyone to snorkel or glass-bottom boat at Biscayne. That's not to say it isn't good, but Pennekamp is the better known, maybe for good reason.

I've swam in the ocean in the keys in January without a wetsuit. A little chilly at first but then it is fine. I'm guessing the water is at least 75 degrees that time of year.

Pennecamp it is, thank you!