"I heard you cry" means you heard the person cry at some point in the past. you heard the whole (crying) event.
"I heard you crying" means that you heard that the person was crying at some point in the past, but you did not hear that person's crying completely -> the action (crying) was in progress or was happening when you heard it but not the whole (crying) moment. you might just be passing when this happened so you don't know if the person continued to cry or not.