Car rentals start at around US$55-$60 a day depending on time of year, size of car, length of rental and from whom you rent. US$100 a day figure you mention would be near the top end of the rental range, for something like a Trooper. Use a credit card that covers CDW to avoid having to pay the US$10-$15 a day CDW charge.
duPlooy's is excellent, with a variety of accommodations from near budget to deluxe. The grounds are beautiful, birding is great, and there is a botantical gardens planted area plus a new orchid house. Judy and Ken duPlooy are good people.
The other places you mention are good, too, in their ways, though they are somewhat different. Green Heaven is a good value, and it has the nicest pool in Cayo. It's on the way to duPlooy's but not so remote, and perhaps not as well located for nature lovers and birds and it's not on the Macal river as is duPlooy's. The owners, from France, are delightful, and they have a good but fairly expensive restaurant with some real French dishes.
Clarissa Falls and Nabitunich are on the Mopan River. Clarissa Falls is on a cattle ranch. Cabanas are pretty basic, but the owner, Chena Galvez and her sister Anna are wonderful folks. The little restaurant here is good and inexpensive. Nabitunich I haven't stayed at for years, but the setting is beautiful, with views of Xunantunich. The Juans who own it also are nice people.
If you don't have a car and don't want to spend a lot on tours, then among these you might prefer Green Heaven, Nabitunich or Clarissa Falls, all of which are within walking distance (Clarissa Falls being the fartherest) from the bus.
If you want to stay in or near San Ignacio, then I would recommend Aguada -- best deal in Cayo for US$25 a day including pool and A/C.
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