Good visualisation of high dimensional data is almost all about the mental model and mapping of dimensions, barely ever about the library. ggplot2 is excellent for displaying high dimensional data in R if you can reason well about your own data. If you can't, no library is going to save you.
If you present an example of high-dimensional data I'd be happy to help you reason about how to visualise it (although this is perhaps better suited to StackExchange).
edit: if you feel you need 3D, you've already failed to represent the data clearly
