All four places -- Log Cab-Inns, Clarissa Falls, Aguada and Nabitunich -- are good. If you want to be close to San Ignacio, that would rule out Nabitunich and Clarissa Falls, though both of these are relatively close to the highway so you could catch a bus. Martha's would be the other choice in this budget category, and it is right in San Ignacio; also, Trek Stop is great, in the same general area as Clarissa Falls and Nabitunich.
All in all, I think Aguada is the best value of the bunch. It's in Santa Elena, a bit away from "downtown" San Ignacio, but an easy bus ride or cheap taxi away. Or you can walk. But any of these are good choices.
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