Am I paying too much rent?

Well, yes, obviously.

Especially now that, per Craigslist, my landlord is offering the suite directly below mine for three hundred dollars less.

So here is one option: call the Division of Housing at 718-739-6400. Ask them for the registration information on your apartment. This gives you the entire rental history for the last twenty years, showing how much previous tenants paid and how many times the apartment changed hands. With that info you can read this factsheet and figure out whether each of the increases that brought the rent up to what it is now, were legal.

I am having some difficulty figuring that out since my negligent landlord suspiciously hasn't registered the rent on my apartment since 1998, at which time the rent-controlled tenant paid.........$95.86. A month.

I'll let you know how it goes.