I think "If he were still alive, he would be 90 years old now" is a better sentence.

They are all fine, but have slightly different meanings, of course. The first sounds like you are talking about the past event in which he died. In the second, you’re not. In the third, it might sound better to change ‘now’ to ‘today’. That way it could still be in the very near hypothetical past.

All are ok. I prefer “if he were still alive he would be ninety now”.

The second one is the best choice.