The show's writer and producer Jeff Davis explains:
Davis said, “A lot of the conflict of the first season is Scott having
to control and hide his abilities now that he’s a werewolf. One of the
reasons we actually chose lacrosse as the sport is that he gets to
wear a helmet and it’s a much more violent sport than basketball. So
we get to hide his features under a mask, which can help, but he still
has to struggle to control his powers because it’s possible for him as
a werewolf to get so worked up on the field that he could almost kill
someone.”
He provides a similar answer in this interview:
One of the reasons we chose lacrosse as the sport is he gets to wear a
helmet — and it’s a much more violent sport than basketball — although
I’ve seen some pretty impressive fights in basketball. So we get to
hide his features under a mask and he gets to race across the screen
at night. So we were able to take some liberties with that with the
sport — hiding him under a helmet.
In another interview he points to multiple reasons:
ASSIGNMENT X: Lacrosse – really? I don’t know of any California high school team
that has lacrosse.
DAVIS: I grew up in Connecticut, and lacrosse was a very big sport at
our prep school. We decided a lot of other TV shows and movies have
done basketball and have done them probably better than I could do.
And I remember kids walking around high school with lacrosse sticks
sticking out of their backpacks and looking like gladiators. They
always looked pretty cool. First of all, lacrosse has never been seen,
and second of all, it’s a pretty violent sport. It was developed by
native Americans as a way to resolve conflicts. They would play it for
weeks with hundreds of players and it would get quite bloody. It has
an interesting history and it adds a certain amount of violence and
energy to the series.