"Upper 3" isn't a standardized term across all private schools. The naming conventions for grade levels vary significantly. It's likely a school-specific designation referring to a particular year group, probably in the upper elementary or middle school range (grades 4-8).
To know what "Upper 3" means, you need to consult the specific school's website or contact the school directly. Their website should have a school organizational chart or a section describing their grade levels.