There are no national organizations that relate specifically to reptile welfare and cruelty cases. Unlike dogs, cats, and domesticated species there are few - if any - regulations in many states that enforce housing/care/veterinary treatment of reptiles and other exotic animals. Generally the focus on reptile keeping tends to be limited to what someone can/cannot own, and nothing related to humane care and housing.
Anyone running an animal-related business *MAY* fall under more scrutiny (such as pet stores and exhibitors who have to have facility inspections and licenses) but these are not always enforced and the line between "private keeper" and "business" seems to get very fuzzy, especially with the many poorly defined regulations pertaining to such things.
When a public shelter/humane society investigates animal cruelty cases, they typically have a contract with a local animal control officer or have a cruelty investigator on their payroll - animal control officers have full police powers which allow them to issue fines, confiscate animals, or take legal action against an offending owner.
Unfortunately because basically ALL reptile-specific rescues are private individuals who offer their time and resources out of their own pockets there aren't many resources to employ law officers to investigate cruelty cases. When a case of animal cruelty is found, we're basically at the mercy of the local state/county sherifs office or the fish & game department to investigate and make the decision on whether or not the offending owner is doing something "illegal"... and the public opinion being what it is in regards to exotic animals, these types of complaints are rarely investigated beyond a single call or visit. The best chance we generally have to actually getting people like this shut down is waiting for them to have in their possession a species that is illegal to keep - This then falls under the jurisdiction of the Fish & Wildlife department - the F&W is generally a bit more enthusiastic to take action against cases like this than regular law enforcement.