While I do like Brandin Cooks, I don't think the Steve Smith comparison is the greatest.
Steve Smith is one of the most unique WRs that has played in the last 20 years. He is a small guy who is really, really long and has a competitive streak that is extraordinarily rare. I don't see Cooks having the ability to win the 50-50 jump balls like Smith has routinely done in his career.
I do think they share the same speed/explosiveness, but Smith (IMO) is a far more effective outside WR than Cooks will be.
Don't get me wrong, I really like Cooks, but would have no fear of him if he went to SF. I'd be more worried about them getting their hands on Odell Beckham, whom (thankfully) most likely worked his way into the top 20.