The two are very different types of places.
Cahal Pech Village is on the top of a high hill near San Ingnacio. It is adjacent to the Cahal Pech ruins but also adjacent to a bar/club which can be noisy, esp. on weekends. The views are very nice from the top of the hill, but this is essentially a town place. The hotel has thatch cabanas and also a motel-like place.
By contrast, Crystal Paradise is out in the "country" on the Cristo Rey road en route to the Mountain Pine Ridge, near the Macal River. It is more of a jungle lodge (though it isn't located in dense bush) and has thatch cabanas and rooms. The Tut family that owns it know a lot about the area, run trips, tours, etc.
The buses can drop you at the foot of Cahal Pech hill (careful of the traffic, esp. after dark), but there is only very limited bus service to San Antonio and Cristo Rey. You would be more secluded here than at Cahal Pech.