I am a landlord in PA and have a tenant who has ben chronically late with payments, so as a result I would drive to her apartment to collect it. There is a statement in the lease that says more than 5 days late paying the rent and you owe a 35.00 late charge. I have never collected it from her, can I deduct this from the security deposit?

No.

Send her a statement for next month's rent including this month's late fee. If she fails to pay it, evict her.

If you have never attempted to collect the late fee, you missed your chance. You can start imposing it going forward. If they don't pay it, you can then deduct what they owe from the security when they move out. But you have to have invoiced them for the amount.