This is an interesting thread. If I were in that position here's a couple of things I'd be thinking:
1. What's you storage/towing capabilities and differences between a 21 & 24 footer? Do you have room to store it?
2. All things considered, I'd either wait to see what the 2017 21 foot boats will be or buy a 24 footer now. I stands to reason that they could be due for an update as they haven't had much attention from Yamaha these past few years. If you get a 15 or 16 24 footer, you also get the articulating keel, Connex, quiet cruise, etc. These boats have the latest in technology, which will likely keep your new boat from being old sooner.
3. As others have said, look around in the general area for another dealer who may be willing to deal. If you can save yourself $1000, it's worth a day of time to go get your boat. I'm in the Bay area and had to go to LA to get mine. Mine was an 09 bought new in 12 so that's where I had to go. If you do, take a friend who is comfortable towing, so you have the option to trade off drivers.
4. As others have said, there are a lot of other brands in the jet boat market now than there were a few years ago. It might be worth comparing the features on those as well. For me, the ability to pop those man-hole covers off and clean out the pumps is a basic requirement and thus why I choose to focus on Yamaha. For others and where they boat, this may not be as important. We all have different needs.
5. Think about what stuff -- dock lines, fenders, anchor (will the 19 work on a 24), cover -- that you can transfer from a 19 to 21 or 24 footer. Get a clear idea of what you'd need to buy new with the boat (a cover for example), and see if you can negotiate on those items.
Whatever you decide, let us know...it's an exciting thought.