How can someone be the greatest heavyweight of an era when most of the biggest, most consequential fights of his time did not involve him?
Let's recap the 1990s and the biggest, most consequential fights. For most of the decade, Lewis was an afterthought.
1990: Douglas KOs Tyson, Holyfield KOs Douglas
1991: Holyfield is the champ, Tyson wins two wars with Ruddock. Everyone is looking ahead to Tyson vs. Holyfield, but Tyson has to pull out due to injuries, and then he gets in legal trouble and goes to prison.
1992: Bowe takes the title from Holyfield in a legendary fight. Negotiations between Bowe and Lewis' camps break down, and Bowe is stripped of the WBC title for not making a mandatory defense against Lewis. Lewis pics up the WBC title, but everyone views Bowe as the real champ.
1993: Holyfield takes back the title from Bowe in a very close fight known for the "fan man" incident
1994: The division is in a state of flux as Holyfield is facing health issues, Lewis's alphabet title got taken by journeyman McCall, Bowe is eating himself out of contention, Foreman KOs Moorer, and all the promoters and sanctioning bodies are really looking ahead to Tyson's upcoming release from prison
1995: More of everyone waiting around for Tyson. Bowe vs. Holyfield III is the biggest fight of the year
1996: Tyson comes back, takes a few titles (Tyson drops the WBC title instead of facing Lewis, and Lewis picks up this alphabet title the next year in a rematch against McCall). Tyson is beating everyone badly and there's no doubt he is the top heavyweight ... until Holyfield KOs Tyson in the biggest fight of the year
1997: Lewis picks up an alphabet title, but nobody cares. Holyfield is viewed by virtually everyone as the champ. Tyson-Holyfield II was the biggest fight. Also, Holyfield picked up another belt by getting revenge against Michael Moorer.
1998: Tyson is away, Holyfield is viewed as the champ and there is nobody left for him to fight but Lewis
1999: Lewis and Holyfield finally fight. Lewis got robbed in the first fight and finally gets what he deserves in the rematch decision.
It's not all Lewis' fault (there were a lot of politics, and Lewis also suffered from not being American and not being very marketable). Both Bowe (in 1992) and Tyson (in 1996) dropped belts instead of facing Lewis. Why? Relatively high risk and very low reward (as I said, Lewis was not very marketable and casual fans in America didn't care about him.)
Having said that, Lewis is not entirely blameless. He could have been involved in bigger fights if he took less money, but his camp were trying to maximize their money while minimizing their risk (just like virtually every fighter's camp, but people like to pretend that this was true of everyone BUT Lewis).