Yes, FB3 Plug-in will run on 64-bit Windows. It uses a 32-bit JRE (came bundled with 1.5.0_11), so in turn requires a 32-bit version of eclipse 3.2, 3.3, or 3.4.
It's been a long time since I ran FB3 Plug-in, so I just installed it on Win7 64-bit, and it still works like a charm. I plugged it into the Java Distro of eclipse 3.4.2 (Ganymede). If you launch Ganymede with the Start Menu shortcut created by the Plug-in installer, the shortcut will launch your copy of eclipse using the bundled version of the JRE.
For plugging into eclipse 3.5 or 3.6, you're better off with FB4 Plug-in, that supports those newer versions of eclipse.