While I would still give the power advantage to Magneto, I am certain Iron Man would put in a good showing.
Magneto hasn't been able to directly affect Iron Man's armor with his magnetism in years. While Mags would still be able to affect him indirectly (throw a train at him) or hit him with other forms of electromagnetic energy, Iron Man's got enough in terms of defense (body armor, force fields, energy absorption) to withstand most attacks.
Even the dreaded EMP, Iron Man's finally been shown to have a partial solution to this vulnerability.
Iron Man has also is own range of magnetic powers, that while nowhere near as powerful as Magneto, can aid him in this battle.
If he had time to come up with specialty armor designed specifically against Mags, I would then give the advantage to Iron Man.
