Depends on what you're after. My guess? If you're coming in from the Caribbean, Boynton's reefs are going to have you wondering if this trip was really necessary. Nicer coral yes, but there are still some spots left in the Keys that blow it out of the water. The one attraction I've found in Boynton that would be worth the trip is the wreck of the Castor, which should still be chock full of goliath grouper at that time of year (and you'll find those in Jupiter, just not maybe in the dozens on one wreck).
Jupiter and West Palm are really something to travel for, in my opinion. The variety of bigger critters is impressive, especially considering it's within a few minutes of a major metropolitan area rather than some isolated island or undeveloped coastline. I've seen more turtles, sharks, and large fish there than the rest of my dive spots put together. That includes the Great Barrier Reef, Southern California, and Grand Cayman. Even before starting on the Emerald (where "you will see sharks" means "be prepared to nudge one out of your face") I mostly abandoned diving anywhere else in Florida on my own time.
As far as ScubaWorks, I haven't had much of a problem with them on Emerald dives. I can imagine why they might be a bit anal-retentive with non-regulars; the dive profiles on Emerald will max out your no-deco time and I was read the riot act once after admitting I went way into deco on my third dive of the day. On the flip side, their steel tanks are filled to the brim and if you request it they can give you some pretty good nitrox mixes (37-38%). The reason I overstayed my time that one day was because I was breathing off a steel 120 filled to 3800 psi; I had a total 90-minute dive with a max depth of 90 feet and still came back up the ladder with 1000 psi to spare.
Overall, I'd say do both if you can. If it's one or the other, stick with Jupiter. If you're confident in your advanced dive skills and experience and don't mind setting out a buffet for the sharks, Emerald is a must. If you're looking for something more low-key where you have time to stop and look around, Capt SL8R, JDC, Narcosis, Ocean Quest, or one of the other charters up in the Jupiter/Palm Beach area will fit the bill.