1989 was an interesting year. Obviusly Becker produced the best standard of tennis that year, and more importantly had the best set of achievements. Thus he was the clear player of the year.
However Lendl's incredibly good day-in day-out consistency that year, meant that he had a pretty strong ranking point lead over Becker at the end of the season. In fact some posters here have shown that even if the ranking systems from the 90s, 2000-2008 or 2009 onwards were used, Lendl still would have had a clear lead in all scenarios.
It's interesting that Edberg in 1990 and Kuerten in 2000 both finished as the year end no. 1 in those respective seasons, despite suffering 1st round defeats at 2 of the majors. Edberg fell at the first hurdle to Bruguera at RG and Volkov in New York in 1990, while Guga suffered the same fate against Portas in Melbourne and Arthurs in New York in 2000.