Monster matchup this.
I'll go for McGrath. There's a few different reasons, including obviously the fact that I've seen virtually every ball of McGrath's career and only segments of Marshall's, and the fact that I find McGrath's style a bit more pleasing on the eye. Really though, in such an even battle I think that the fact that McGrath has played in such a batsman-dominated era counts in his favour. If you compare his record to the others of his time, he's rivalled statistically only by Murali, who gets quite helpful conditions for his style of bowling for plenty of his games. McGrath has succeeded as a seam bowler with no great pace in an era of flat pitches, dominant batsmen and high scores, and maintained a record in the process that puts him among the best of all time on a statistical basis.
I'm also a great admirer of the fact that while McGrath is a bowler who gets a large portion of his wickets through consistency, accuracy and subtle variations, much like someone like Hadlee, he is also possibly the best exploiter of seam-friendly conditions in the modern era. While McGrath is good on a subcontinent road or mid-season Adelaide on day 1 or whatever because he can bowl 20 overs for 30 runs and take a wicket or two in the process, he's also virtually unplayable on those rare occasions in the modern cricket world where he actually gets a helpful surface. His ability to absolutely dismantle teams at Lords for instance (a place which suits his bowling quite well) is absolutely amazing, with performances like 8 for 30 odd in 97 and 5 for 1 in 05 at that ground. One has to imagine that if he played in an era where more pitches suited his bowling he might have been an even more successful bowler.
Marshall followed in the footsteps of some of the greatest fast bowling attacks and at times improved on them, and is no doubt he is one of the finest fast bowlers of all time. Against any but 3 or 4, I'd vote for him, but in this case it's McGrath.