Once you get the Lockjaw up the higher deck, the green gem combo is indeed easier than the fish one. But if you take exactly the right pause between the fish in that bit, you can get lots of points with it. A combo of 3100 is possible, and every fish you can get in combo is worth 300 points at this point. I believe I got a combo of 4000 once.
After this combo, you have to keep making combos of 60 for the fish on the higher deck, and you can make combos using the pauses correctly too, with the other three cannons. I made a combo of more than 900 once using only the fish from those three cannons. lol, it's pretty hilarious...