All I can tell you is what we have done and are doing this time:
GC: renting a car and driving the island ourselves
Cozumel: actually booked a RCL tour...All terrain truck and snorkel tour. We originally had a snorkeling tour booked thru eagle ray divers but decided against just plain snorkeling and ended up with RCL instead....we normally don't use cruiseship tours due to such crowds but we saw that tour and kinda liked it
Labadee-Just hanging out at the beach, relaxing, etc...no tour here
Jamaica-Private tour with Pete Taylor who was recommended on cruise critics message board. Seems to be good and he can show us personalized places and he's taking us to Dunns River Falls too.
We have been to cozumel and GC 3 times already.....1st time in Cozumel we took a Tulum Tour and that was nice BUT the drive there and back was LONG...the ferry ride sucked (rough ride) to the mainland too. 2nd time in Cozumel we did a 4x4 jeep/caverns tour in the mainland and that was FUN too...we got to drive our own jeep and jump in the caverns (VERY COLD water) and see some of the natural sites.
The 1st time in GC we didn't do any tours that I recall, but the 2nd time we the stingray city sandbar with nativeways. That was really cool and we took our 10 yr old daughter and she thought it was awesome.
Hope that helps. We have cruise pics and info on our homepage if you want more ideas with photos, etc...