Just a thought...
If you rent a jeep and it breaks down...the people on the boat will wave goodbye as they leave! Taking an excursion...and a jeep breaks down, there's someone to bring you back or at worst, notify the ship there's been a problem.
We took the Eco Jeep and Snorkel and it was wonderful. Had a great time, incredable coral reef for snorkeling, crocodile and ruins stop on the way back..I highly recommend it.
You can also do the rental thing and have a wonderful time. It's up to you.