Just look at their historical WAR from baseballprojection.com. From 1990-1999 Griffey's was 65.9, Thomas' 54.3. I'm a little biased because I'm a big fan of positional adjustments but I think Griffey is the clear favorite. I really want to agree with you because Frank Thomas seems to be eternally underrated, but I just can't.

The question, specifically, was whether Thomas or Griffey was the best AL player (read the opening sentence, which excludes Bonds) of the decade. Not which one was best relative to the other players at his position.

I see some value in your comment but it seems to miss the point of the post.

There is just so much I disagree with in this post. But first an interesting anecdote: my father being from Gary, Indiana, growing up I always was caught up on Chicago sports. One day I was at the O's game and Frank Thomas struck out with two outs and the bases loaded (he was never known for being clutch). I turned to my father and said, "He's just not having his best year". In fact, he was having his best year (at the time at least). It was 1993.

As for the analysis:

For one, he doesn't account for position value at all. To have a power hitting center fielder is a significantly more rare commodity than first basemen. Yes, Thomas was great but he was a one of many power hitting first basement in the steroid era. The same isn't quite as true for, say Albert Pujols, because power hitters are more of a rare commodity then they were then. He is definitely right to warn against overrating Griffey's defense (gold gloves are meaningless See: Derek Jeter, and to a lesser extent Michael Young). But it doesn't change the fact that to compare their value over a replacement player at that position would show that Griffey is by far superior statistically. The biggest argument, which he doesn't bring up, is FT's favor is durability. Griffey spent a lot of time on the DL which one can argue hurts his value but, at the same time, makes his numbers seem that much more ridiculous.

All that aside, the debate just seems silly to assume that either of the two are the best of their era. To warn against overrating Griffey due to the media darling-hood, but to then not even mention maybe the most underrated player ever (due to media bastard-hood) is contradictory. I think without a doubt Barry Bonds is the best player of the 1990s, if not the best player ever. Before the 90's even began. He had amassed over 100 steals and almost 100 home runs. He hadn't even taken off yet. If you want to get in the steroid debate, you have to include every player in that era. (For the record, athletes were using Monkey steroids in the 1930s… the steroid debate is pretty stupid–it is the nature of the athlete to get any edge possible) Overall, the media–and probably history– is far too unkind to unsympathetic players who used steroids, and far too kind to sympathetic players who used steroids. If you're just looking at who the most valuable player was in the 90's, it is without a doubt Barry Bonds.

Anyone ever throw Albert Belle in the mix? Loathsome, but pretty good.