To be clear, Nadal's foundation is in a charitable relationship with an arm of Laureus's children's charity. It's a bit of a stretch to call that a "business" relationship. Laureus was founded by Nelson Mandela. So you can ask yourself why Federer, whose mother is South African, has won it so many times, too. If you want to be that conspiratorial about it.
But to the more direct point of Nadal being the best candidate for the award: You say that winning 13 titles at one Major is more equivalent to some kind of lifetime achievement, rather than athlete of the year, if I'm reading you right? But, firstly, Nadal's career isn't over, and he may yet win more there. And you may personally have preferred Lewandowski, but he plays a team game, and what he achieved was, in part, a group effort. What Nadal did was single-handedly beat any record by man or woman in singles (normally-abled) tennis. All by himself, and despite great odds, he won Roland Garros again. Last year. And that record begins to transcend his own sport. You may prefer football, but what Lewandowski accomplished doesn't even come close to, say, Messi's best year. The only other nominee with an individual world record was Joshua Cheptegui, so he should have been your other pick. Don't make it about some faked-up inside deal. What Nadal did was bigger than tennis. He deserves the award.