I have dived the reefs from Jupiter to Key Largo, and I prefer Boynton Beach for the most COLORFUL reefs, and plentiful sealife. Sure Key Largo is popular, and famous, but there's no comparison. The reef in Boynton might be the best reef in the state of Florida - if you like to see a colorful reef covered with sponges of all shapes and sizes, and tons of fish.
If you like monochrome reefs, and large brain coral and elkhorn coral... By all means go to Largo. If you want to dive some great wrecks like the Duane, Eagle, and the Spiegel Grove - then go to Largo.
But the East Coast of FL - North of Largo is GREAT!
I've tried several dive ops on the coast, and my favorite is Splashdown Divers in Boynton. They are the most professional, helpful, and friendliest operation I've been with maybe anywhere.
Whatever you choose... Have fun!
Edit - I have video from both Boynton and Key Largo in my gallery if you want to see the difference.