A very fair comparison using career stats would be Sammy Sosa. I have no proof that Thome ever did steroids, so he is safe from that criticism. Sosa was doing steroids though, and his numbers got a boost from the performance enhancing drugs he was using. Particularly his record chasing homerun seasons in 1998, 1999 and 2001 were aided by steroids, as were Mark McGwire and Barry Bonds, the players that were besting his numbers. But lets look strictly at the numbers, and determine who has had the most successful career.
Sosa came into the game as a 20 year old playing for the Texas Rangers before getting traded to the Chicago White Sox the same season. He was acquired by the Chicago Cubs in a trade for slugger George Bell at the beginning of the 1992 season. He had a decent year for the White Sox in 1990, playing in 153 games, hitting 15 HR and 70 RBI. He hit only .233 though and struck out 150 times. He had a breakout season for the Cubs in 1993, hitting .261 with 33 HR and 93 RBI. He became a star from there, holding his own in the strike-shortened seasons of 1994 and 1995, then hitting 40 HR in 1996 and 36 HR and 119 RBI in 1997.
Thome broke in as a 20 year old third baseman with the Indians in 1991. After being a bench player for his first three seasons, he finally got a chance to play every day in 1994, hitting .268 with 20 HR and 52 RBI in the season that was shortened due to the player's strike. He started his homerun hitting run in 1995 when he hit 25 and drove in 73, then in 1996 hitting 38 and driving in 116 and 1997 he hit 40 and drove in 102. He has maintained consistant HR numbers since, even when his role has been reduced over the past three seasons.
So, breaking down the career numbers, Thome has played in 2485 games while Sosa played in 2354. Thome currently has 604 homeruns while Sosa hit 609. Sosa was a .273 career hitter while Thome has hit .277. Thome has drawn 1725 walks over his career while Sosa only had 929. They both struck out a lot with Thome leading 2487-2306. Sosa only played 18 seasons while Thome is entering his 22nd. The most homeruns Thome hit was 52 in 1992, while Sosa hit 66, 63 and 64 in seperate years.
Thome is a rewarded product for his longevity. Sosa was a talent, even though he did steroids in the steroid era. While that will be held against Sosa similar to Mark McGwire and Rafael Palmeiro when it comes to making the Hall of Fame, Thome seems to be a no brainer. The writers may hold out the first season because of the era he played in, but his numbers have to be considered legit and he is a Hall of Famer. Sosa was the star player on the Cubs while Thome played in the shadow of Albert Belle and Manny Ramirez. He was the lone power hitter on the Phillies teams he played for and held the same role for the White Sox. He has been a role player since 2009, but has maintained respectable numbers. Sosa returned to the Rangers in 2007 after sitting out the 2006 season and has a nice season hitting .252 with 21 HR and 92 RBI showing he could still play, perhaps not on steroids.
I think stats wise, both players are fairly even. Thome owns the higher on base percentage and has a chance to pad his numbers a little more before he calls he quits. Sosa, unfortunately, will be known for the time he played as well as his performance in the congressional hearings. If he was known to be clean, he would be a HOFer, but we all know he wasn't. Its hard to guarantee any player was from that time, which is why its fair not to put Thome in that class without any proof. Thome wins the battle of the numbers by a narrow margin, as Sosa gets credit for always being the best player on his team and being one of the best sluggers of the time period. But, Thome is the better player and a Hall of Famer while Sosa is not.