I am trying to do some intersection tests and so the math gets weird if two certain points have the same $x$ coordinate and so infinite slope. The points can be anywhere in any quadrant.
I want to "rotate" all my points through $90^o$ which will preserve what I need while making the math easier.
For a point $(x, y)$ is it just changing it to $(y, x)$?
No: replace $(x, y)$ with $(-y, x)$. That will rotate 90 degrees counterclockwise about the origin.
What you proposed will flip everything around a 45-degree line that runs from southeast to northwest.
BTW: To rotate clockwise, replace $(x, y)$ with $(y, -x)$.