I've done 7 1-week trips to Bonaire over the years (well over 100 of my dives were Bonaire), most recently April '13. I've done
1 trip to Key Largo, diving with Rainbow Reef Dive Center for 5 days, getting in 20 boat dives in late Sept. '13. I loved both. Comparing Key Largo to Bonaire, some tips from me:
1.) It's boat diving rather than shore, but you can do 2 boat tips per day (with Rainbow Reef Dive Center, anyway), and get in 4 dives/day. It's not Bonaire's 24/7 anytime/any site diving, but plenty for me.
2.) Rainbow RDC puts guides in the water; I get to see more stuff.
3.) Of the 20 dives, 3 were
Spiegel Grove and 1
Duane, so 4 'deep wrecks.' Lower viz. & some current, so a bit more involved than a
Hilma Hooker dive; for example, you go up & down a mooring line.
4.) Key Largo reef dives tend to be shallow; whole dive might run around 20 - 40 feet deep.
5.) Whereas Bonaire sites are sloping hills, Key Largo's bottomography was, in my limited experience, mostly flat. We did one dive that was similar to the typical Bonaire reef look, and it was actually pretty deep.
6.) I agree Key Largo's reef sites seems to have more fish biomass.
7.) If you want to see fish, and have AOW, don't discount the deep wrecks. That's were you're more apt to see Goliath Grouper. If you haven't before, worth a look.
8.) Species differ; in Key Largo, I saw things I didn't in Bonaire - Atlantic Spadefish, Hogfish (though I saw Spanish hogfish in both), Grey Angelfish, Black Grouper, Goliath Grouper, 2 Nassau Grouper, Porkfish, Caribbean Reef Sharks, Nurse Sharks.
9.) I saw more blue striped grunts in Key Largo, though Bonaire doesn't lack them. I saw more large barracuda in Key Largo. Also saw more big green moray eels.
10.) I saw sea cucumbers in Key Largo, but not as many as Bonaire.
11.) I saw a good deal more rays in Key Largo, and got close to some big brown ones on the sandy bottom (one I assumed was a southern, but our guide told me due to body shape, it was a ridgeback stingray).
12.) Key Largo viz. was not as good as Bonaire. I'm guessing maybe 30 - 50' vs. 75 - 100'?
13.) A few of our Key Largo dives were drift dives, though most were not. It's nice, and you're not committed to as much drift diving as you'd likely be doing in Cozumel.
14.) My dive times tended to run around 50 minutes or just over, less on the deep wrecks.
15.) To surface and re-board in Key Largo, we'd surface & grab a long line off the back of the boat, and pull ourselves to it. In the first few feet of water, there are often moon jellyfish; dinner plate-sized jelly fish with short tentacles that can sting humans. You can put them aside by the bell; I used a fin, but I'm told you can do it by hand. From what I understand, stings are painful, but not excruciating, and not usually considered dangerous. People try to avoid them, but don't seem particularly afraid of them. It adds a bit of adventure to the diving.
If you've already been to Bonaire, I'd suggest you give Key Largo a whirl up in the summer or fall when the water's warmer.
Richard.