1. sounds like you ARE seeing him now. 2. is most natural, if you mean that you still haven't seen him.

They are both good but have different meanings. Say #1 if you now see Ali or expect to see him very soon (like in the next 30 minutes) Say #2 if you do not yet see Ali but may see him in the future.

2

Depending on what you mean, I would instead say, “I haven’t seen Ali yet (today, this morning, ec.).”