Scarface is an awesome film that has gotten a bad wrap since that shitty MTV show Cribs started and every shitty rapper ever on there showed off their Scarface DVD. It made the film way too glamorized, whereas before then it could have been considered a cult classic, which is what it should be. The fact is though, Scarface is one of the greatest gangster films ever made, period.
The Matrix, on the other hand, is one of the greatest Sci-Fi films ever made itself. Hell, it's one of the greatest action films as well, if you want to put it in that category. It's mysterious, exciting, and compelling all the way throughout. Did the crappy sequels bring down the original? Not for me personally it didn't, so I can't use them as an excuse here to vote for Scarface.
To me, it's much harder to make a truly great Sci-Fi and action flick than it is to make a great gangster film, which is why The Matrix gets my vote here. As far as which film I like the most... they're pretty much tied. Both are definitely in my top 25 favorite films of all time. But, I have to give the edge to The Matrix since in the grand scheme of things, I think it has much more to offer than a film like Scarface. Scarface is pure entertainment, but not much more more. The Matrix is also great entertainment, but also thought provoking and absolutely compelling.