You are lucky in that most of the diving from Jupiter down to the Keys is great: if possible, an optimal dive vacation would be to rent a car and stop in several places along the way. I dive in Jupiter a lot and use Jupiter Dive Center regularly. Jupiter is the place you are most likely to see big marine life such as sharks, turtles, rays, big morays, etc. Jupiter is well worth diving for a few days.
But if you want to stay in one hotel and not move around, I'd definitely look at the Keys. I usually make 2-3 trips each year (long weekends) and get in 8-16 dives per trip. If the diving is most important to you, then Key Largo is the right place. I dive with Conch Republic Divers most of the time when I'm in the Key Largo area (but have used other good ops like Silent World too). From shallow beautiful reefs to deeper wrecks along with a couple of deep reefs like Conch Wall: Key Largo has it all. Plenty of good places to eat, but you'll have to drive since the upper Keys are not really walking friendly.
If you are more interested in top side activities with diving as a secondary pursuit, Key West is the place. The dives are not as nice (though the Vandenberg wreck is pretty cool), but there are more taverns, restaurants, and bars per capita in Key West than anywhere else on this planet (that's a little exaggerated, but not far from the truth). KW also has some interesting tourist actives like the Hemmingway House, Eisenhower White House, museums's, etc. and Key West also has the better beaches: most of the rest of the Keys have crappy beaches, if any at all. The only dive operator I've recently used in Key West is Captain's Corner.
Anywhere in the Keys will also have activities like jet skis, fishing, kite boarding, etc.
If you are doing a multiple location trip, I'd fly into Miami, Ft Lauderdale or West Palm Beach. If you are only going to Key Largo, I'd fly into Miami or Ft Lauderdale. If you are only going to Key West, I'd try to fly directly to Key West. While Key Largo and Key West are only separated by 100 miles or so, at certain times of the day/year, it can take 3 or 4 hours to drive from one to the other: its a pretty drive over the overseas highway, but frustrating if you are in a hurry.
So here's my perfect itinerary
-Arrive Friday and dive in Jupiter on Saturday and Sunday. (dive op: Jupiter Dive Center, plenty of hotels like Holiday Inn Juno Beach, Best Wester Jupiter or check out South Florida Dive Journal's website for more suggestions)
-Dive Monday morning in West Palm Beach, Boynton, Pompano or Ft Lauderdale. (Force-E can arrange a boat in any of the locations, Underwater Explorers for Boynton, Jim Abernathy for West Palm Beach, Pompano Dive Center, Scubatyme or South Florida Dive HQ for Pompano/Ft Lauderdale)
-Drive to Key Largo Monday afternoon. (Ocean Pointe Suites is a nice place to stay)
-Dive Tuesday-Thursday in Key Largo and Islamorada (Conch Repubic Divers, Silent World)
-Drive Thursday evening to Key West.
-Dive Friday and Saturday in Key West and or Looe Key. (Cap't Corner but other SB'ers will provide additional suggestions)
-Fly home Sunday evening.
Alternate: add a live aboard like MV Spree's 3 day weekend trip to the Dry Tortugas some point during your stay
