These are two great playoff runs. I'm surprised the voting is so one-sided (currently 9-2 for Leetch).
Their offense is comparable, but Leetch was on the ice for 22 ES goals against, compared to only 11 for MacInnis. There's a lot of context that goes into a number like that, but at a high level, both teams allowed roughly the same number of goals against in the regular season (226 vs 231). And even though Leetch was on the ice for significantly more goals against, the 1994 Rangers got much better goaltending (92.2% save percentage) than the 1989 Flames (90.3%). Plus, Leetch played most of that playoff run with a rock-solid partner who was focused solely on defense (Beukeboom).
It seems like MacInnis produced nearly the same output (1.48 vs 1.41 PPG) but was on the ice for half as many goals against (while playing in front of weaker goaltending). This seems to suggest that MacInnis was better.
I think the main thing explaining the goals against is simply deployment. Leetch was obviously Keenan's go to guy in all situations including defensively as the video I posted called out. MacInnis did not seem to be the defensive matchup guy on his team then, where you had a couple other guys usually taking that role.
Goals for/against is much harder to isolate than scoring though, and while MacInnis had 8 even strength points (2 goals) Leetch had 20 (7 goals). I feel more comfortable to say that the double up difference in even strength scoring was due more directly to Leetch's abilities vis a vis MacInnis, as compared to the double down goals against being due directly due to MacInnis defensive abilities vis a vis Leetch.
Although I will note that Calgary's other star defensemen Suter went down early in the playoffs and MacInnis really picked up the load from him which is a definite point in favor, and it was this event which probably led to Calgary use MacInnis more going forward and cut Suter loose.
Side note, is there any place the old goals for/against stats are available for the playoffs online that you are getting them from, or did you have the data handy from before? I know the NHL site used to have them like over ten years ago but removed it when they redid their boxscores and updated the stats a bit (had some changes to the historic plus/minus).