The polymake package is to be installed in a usual way with pkg_add command. The package is relocatable, you can install it at a different location than /usr/local/polymake if you add the -p option.
If your computer is amply equipped with RAM, you might consider to compile polymake yourself and tune the compiler optimization for your CPU model. Then you must pick the port tarball, unpack it in /usr/ports/math, edit the compiler options in Makefile, and finally run make package. Again, you can set an alternative installation directory by adding an option PREFIX=DIR .