For what I can see in OpenCV documentation, this is a reference-counted smart pointer, essentially, same as boost::shared_ptr. Even it uses atomic operations on the reference count.
I would make the choice based on portability and interoperability.
- Is your system going to be ported elsewhere and depends on OpenCV for sure but not on - boost?
Then, stick to OpenCV- cv::Ptrif you can avoid boost and you get rid of the dependency.
 
- Does - boost::shared_ptrplays nice with the rest of OpenCV?
If you have something returning a cv::Ptr from OpenCV library, maybe it's better to stick to cv::Ptr   in these cases, because the reference count will be handled incorrectly if you mix both kind of  pointers and the resource could be destroyed prematurely.
 
- You're going to stick to - boostwherever you port the project?
Then, stick to- boost::shared_ptrwhen you can do it, it's more standard, people know it and will immediately understand your code. UPDATE: In C++11 you have std::shared_ptr, which amounts to no dependency if you can afford it, so you can use std::shared_ptr in this case and get rid of boost also.
 
Just as a side note, there is a technique to mix boost and std shared pointers that can keep the reference correctly around and could be useful for someone. See this question, it could be relevant also for mixing other kind of reference-counted pointers: Conversion from boost::shared_ptr to std::shared_ptr?
In my experience, when you port something, the fewer dependencies, the better, or there are certain platforms for which compiling can be a hell. So make your choice based on portability if it's a concern and interoperability of pointers with libraries.