"I heard you cry" means you heard the whole thing from the beginning to the end "I heard you crying" means you heard some part of it when it was already in progress

"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.

crying can be both past and present. "I heard him crying or I heard him cry" are both acceptable. cry can be used for future tense though "I could see he was going to cry"