Bleeding Edge Iron man can take on all the thugs, ALL of them. A weaker version of his armor tanked a nuke at 2% shielding. His Bleeding edge armor is quite simply beyond the capacity for thugs to harm him at all.
Punisher takes around 50 to 100 thugs in ten a wave increments barehanded. With ammunition, you can add a thug for every bullet he has, provided we're not talking bullets that can take out multiple targets.
Wolverine probably tops out at around a 1000 or so all at once. His healing factor allows him to exert himself for extended periods of time, but even his stamina has limits. I'd say he'd eventually get overwhelmed and taken down. Granted, they couldn't keep him dead, but they could keep hurting him before he could heal so severely he can't retaliate. Provided they maintain shifts. For all eternity.
Iron Man, however, when Tony gets tired of blasting thugs, he switches over to JARVIS autopilot and let's him finish it while Stark takes a nap. All the thugs go bye bye.