The suggestion that Vani gave is widely used in most IT companies. Is your company a start-up?
Additional Suggestions for Managing Late Arrivals
Another couple of them in vogue are:
1. An employee can come late if he/she has prior permission from his/her boss for staying late the previous day. This ensures that the boss is aware of it and has some amount of control over the situation since HR wouldn't be tracking the late-comings on a minute-to-minute basis.
2. Implement some sort of incentive/award for those who have absolutely no late-coming record, similar to what we have in some schools, to encourage latecomers to correct themselves.
And finally, if none of your actions, including any rebukes, work, maybe you need to be tough on him, at least to ensure he doesn't become a wrong example to others later.
Regards,
TS