Studying baseball statistics is really an interesting practice. I find it to be pretty interesting that the sport that relies most heavily on statistics, and the one in which peoples' statistics are used to judge them most heavily is also the sport where the statistics between players, teams, and eras are the least comparable from an objective standpoint.
Let's take the largest, and probably least relevant, issue, steroids. Assuming a lot of gies were taking steroids circa 1990 through 2004 and were not taking them much outside of this window, then those stats are, in one way or another, skewed. How much they are skewed is really beyond the scope of this post. It also seems like something that would be really hard to determine, certainly from my perspective, but just aknowledging that they are skewed is enough.
The more important issue here is really the arbitrary nature of the baseball field. Can you imagine in the NBA if you went to Boston to play the Celtics and whenever you went there the basket was 9 ft. high istead of 10? And going into Cleveland the court was an extra 20 feet longer. And in Phoenix the 3 point line was 5 feet farther back. All of those are ludicrous notions, but in baseball they are completely acceptable. Guys who call themselves "purists" will tell you that's what adds to the charm of the game. I'm somewhat surprised that no one makes a bigger deal of this to be honest with you.
If Joe DiMaggio didn't play in Yankee stadium with a 500+ ft. left-center field, he would have had conceivably hundreds of more home runs. If Babe Ruth didn't play in Yankee Stadium with a 300 ft. right field porch, he would have certainly had fewer home runs. Nearly every stadium built since Camden Yards has shrunk the dimensions of the field it replaced, and made it far easier to hit home runs. There are some exceptions, PetCo Park in San Diego and the new CitiField come to mind, but for the msot part fields are shrinking. Would Ryan Howard be nearly as valuable a player in any other stadium? Ryan Howard must hit more opposite field home runs than any other player in baseball. He's got tremendous power to the opposite field, but it doesn't hurt that they play their home games on the Clubhouse Field (Clearly the Middle Field would be more conducive for MLB games).
Home runs is the easiest statistic to point to relative to the arbitrary nature of each field, but is certainly not the only statistic that's affected by it. Smaller fields mean fewer doubles and triples. Different size fields mean different defensive alignments, and what I'm sure are significant differences in fielding percentages and assists, put outs, things of that nature.
The point here is that comparing gies from the days when a lot of fields were cavernous to today when fields are much smaller, and comparing guys directly who play in different home stadiums is, in many respects, and exercise in futility. No one tries to control for field size or other conditions that confound the statistics. I'm not saying they should, but then we should also not point so heavily to those statistics when we talk about baseball players.