Right answer:
Había tres manzanas sobre la mesa.
When you use the verb haber to indicate the presence or existence of people or things acts as impersonal and hence this is always used matching the third person singular, which is había. On the other hand, the number tres acts as an adjective telling us the number of apples. Moreover, sobre is a preposition that means on. Finally, we can write this sentence as follows:
Había tres manzanas sobre la mesa (There were three apples on the table)
