If you just look at the overall performance of the Trump campaign, it gets pretty low marks. From the confrontation with the Khan family to Trump's tendency to shoot off his mouth, he's not getting great advice. Manafort is the head and now he's embroiled in the Ukraine money controversy. If he really wants to do what's best for Trump (and I hope he doesn't, since I can't stomach the thought of president T) then he should resign.
Yes, Manafort should resign because the New York Times article seems to be a "smoking gun." He reportedly received millions of dollars in illegal payments from Ukraine. If this was the campaign manager for Hillary Clinton, Trump would be calling for the person to step down or for Clinton to fire the person. He should resign, but he's following the lead of his candidate, so he probably won't.
Donald Trump has selected Paul Manafort as his campaign manager. Obviously, the opposition is going to launch personal attacks at anyone who works for the Trump campaign. That does not mean Manafort should resign. He is in the position of campaign manager. It is up to Trump to decided whether or not he keeps that position.
Manafort should stay in place. This is because the media is always demanding that people step down, be demoted, or apologize to for imagined violations or political incorrectness. Manafort does not work for the government, so I am not concerned about his actions with the Ukraine. I think this scandal will soon pass.