I also agree that if you're going to be in the area anyway, all three are a must! There is such diversity in each area. Jupiter (being partial here) is my absolute favorite, as I can always count on seeing sharks (nurse, reef, lemons [in season], bulls [especially when spearos are around], turtles galore, Goliath Grouper, moray eels, lobster (that taunt you out-of-season because they know you can't touch them.....lol), lots of tropicals, stingrays, etc, etc, etc. Never a dull moment! My charter of choice is
Scuba Diving Jupiter with Jupiter Dive Center, Scuba diving lessons at a PADI 5 Star facility, daily scuba diving trips in Jupiter, Florida.. (Again, I'm biased with this center, as they have always provider stellar service.....and I happen to dive guide for them).
Blue Heron Bridge is a must-dive shore dive! As mentioned above, it's free, and a dive that one will never forget! To look at it from the land, it looks like nothing special, but go beneath (9'-20' tops), you'll find seahorses, spotted eagle rays, bleenies, frogfish, starfish, octopus, flying gurnard, batfish, peacock flounder, stargazers. and a host of other incredible creatures! Diving at slack high tide is a must to enjoy this spectacular dive.
West Palm Beach is awesome for shallower dives. The Wetter the Better, Little Deeper, Jim Abernethy, are the three fantastic operators that I've dived with in the past and highly recommend.
Boynton Beach, nothing but the best is diving with Kevin on Underwater Explorers. The reefs are prettier there than in the northern spots, but the sea life is equal or less diverse. The wrecks are better there and in West Palm than any other place (barring the Keys, of course).
Please plan an extended stay in the area and enjoy each dive the Jupiter-to-Boynton Beach area provides. Guaranteed to not disappoint you!