D is incorrect. The Yankees have won more than 25% of all world series ever played (it was exactly 25% before last year, then they won again). The Marlins have won twice in 16 series (1993 through 2009, but no WS in 1994 due to the strike). That's less than half championship percentage the Yankees have. The Marlins have won both of their World Series appearances, but with only 2 appearances, the odds of that are 1/4 even if it's pure chance. The Yankees have won 27/40, more than 2/3 of each opportunity. The only team with more than 2 appearances with a better winning percentage than that is the Pittsburgh Pirates, who won 5/7, but haven't won in over 30 years.
The stats for the greatness of the Yankee franchise are simply overwhelming. As some have put it, if you want to compare them to a dynasty, the only one appropriate is the Mings. Certainly not a late-comer upstart like the Marlins.
If you look year to year, that's a different question. In 2003, apparently the Marlins were better, as they played head to head in the world series. In 2007, the Marlins also won and apparently were the top team. The Yankees have been on top 5 times since the Marlins formed, winning their division almost every year (something the Marlins have never done, having won the wild-card in both years they reached the post-season).
Yankees by far. More history, titles, winning, players. The only argument the Marlins can make is that for a young franchise they already have 2 titles. And the fact that the 2 years the Marlins made the playoffs, they won the whole thing. But the Yankees are so much better in every way... Marquee names, records, pinstripes, global presence and recognition, etc.