Boris Becker with just 12 weeks
As a 6-time Slam champion often slotted somewhere in the Top 10, this is the best argument of how a great player can be denigrated because their best achievements coincide with better consistency from another all-timer. In this case it was namely Lendl who stole as some would claim numerous weeks from Becker's resume. In total, 6 players with 4 or less Slams had more weeks at the #1 spot than Becker while contemporary Edberg with the same amount had 60 more.
Lleyton Hewitt with 80 weeks
On the other extreme we have Hewitt who not only garnered 80 weeks overall but 75 consecutively, a mark only bested by 5 other players. This of course occured during his 2 year peak where he won 1 Slam in each year but also captured the WTF and had 5 deep runs at the Masters both years too. This came in what many refer to as a transitional era where simply put no other players was able to manage the same consistency with Sampras on the decline, clay court specialists vulturing there and the biggest challengers being Agassi, Ferrero, Kuerten, Kafelnikov(01) and Safin (02).
Mats Wilander's 20
Becker's 12 weeks despite 6 Slams has been mentioned but Wilander's 20 with 7 is just as bad if not worse considering when he captured the #1 and for what. Unlike the many gents who only got the #1 due to the right concentration of winning, Wilander needed to capture 3 Slams to garner the #1 and was only able to hold it for exactly those 20 weeks and never again. He lost it shortly after the start of 89 when he failed to defend his AO title losing in the 2nd round but he still held 2 Slams and 2 Masters while Lendl upgraded his previous year's SF to a win he would drop slightly at the French from QF to 4th. Lendl's amassed secondary titles however was simply too much as when he took the mantle from Wilander he held on to it for 80 weeks despite only winning 1 more Major.
The ATP ranking generally rewards the most consistent players.
Boris Becker I think he had a problem of consistency during the year, in the sense that often he was distracted and lost in the first or 2d rounds. It did not happen to Lendl.
Wilander has always been very competitive but not very consistent (a bit like Becker) and tended to lose a bit too early for a number one.
His 1988 season was exceptional (3 slam + Lipton) but short.
It also depends a lot on the circumstances, in the sense that it may happen that during the best period of Becker, it was also the best period of other more consistent players (Edberg, but especially Lendl who rarely lost in the first rounds). So it could be that Becker was better but less consistent,
Lleyton Hewitt, on the other hand, was perhaps more consistent and in his best period confronted with less consistent opponents.
Sampras, for example, has remained number one many years but with a not very high average consistency. This is because his opponents had a fairly low consistency.