Adapting from the wiki:
mkisofs -l -J -V TC-custom -no-emul-boot -boot-load-size 4 -boot-info-table -b boot/isolinux/isolinux.bin -c boot/isolinux/boot.cat -o /tmp/TC-remastered.iso /mnt/hdaX
This assumes your partition is mounted at /mnt/hdaX, and that you have added your desired boot codes to boot/isolinux/isolinux.cfg. If you'd like to boot the cd with grub instead of isolinux, please see the grub docs for that.
Edit: please move the boot folder to the partition root before that, isolinux can't find it if it's in /tinycore
Edit 2: mkisofs is in mkisofs-tools.tce