Since Whonix 0.6.1 (Developer Preview version), it's trivial to create 64 bit builds of Whonix. If you already know how to build Whonix from source code, only a very few steps are missing.
Simply get into Whonix build-steps folder and open the 20_create-debian-img step.
For example, you can comment out.
And comment in.
Despite it's name, the "amd64" architecture, works on both, AMD and Intel.
NOTE: Its impossible to create 64 bit builds on 32 bit hosts. So if you want to create a Whonix 64 bit build, you most likely want to install Debian Wheezy 64 bit first (in a VM).
Also interesting architectures for custom builds: Kernel of FreeBSD. It won't work out of the box for Whonix-Gateway, because Whonix Firewall is based on iptables (Linux) and the FreeBSD does not support iptables. It's firewall is pf. The Whonix iptables rules would have to be rewritten in pf.
For Whonix-Workstation you could also try "kfreebsd-i386" or "kfreebsd-amd64", but this is untested, just as 64 bit Linux builds are much less tested.
Most credit and thanks goes to upstream projects, the Debian and grml-debootstrap maintainers. The Whonix specific modifications where trivial, it's only required to replace variables and to document it.
It will probable still take a long time before The Whonix Project will offer ready to download 64 bit and/or Kernel of FreeBSD based builds. I don't think it will be possible without a new contributor jointing the project to provide for those builds. Creating the 32 bit i686 (and i486 compatible) version, testing and uploading already takes much time.