Is it safe to list my publications on the Internet if I am being stalked? I am being stalked by someone who probably poses no physical threat to me, but his actions were concerning enough that we filed a police report, and the dean of students moved me to different housing.

Do you think it is worth taking my academic website off the Internet?  With my publication list, my stalker could find the names of my collaborators, and the name of my PhD advisor (who already knows about the situation).  There is a tiny chance he might contact some of them.
There's a small chance it might help but probably not. 

If your page has been on the internet for any length of time then it's already going to be stored in a number of library archives  like archive.org

It's possible to remove pages from the site but it takes time and there are other archives.

Example:

http://web.archive.org/web/20141124181833/http://www.statcan.gc.ca/pub/12-591-x/2009001/02-step-etape/ex/ex-publication-eng.htm

Also your publications are likely to be searchable through a number of online systems for finding papers such as google scholar.