Dr. Henry Thomas (whpthomas) has created a command line utility to convert Makerbot GCode to x3g files. I have compiled that for Windows using MinGW, and it seems to work fine.
You can download the latest version here: gpx.exe (commit e150d0)
Commit e150d0ede0386a23173d399d6174cd037dd88f82: gpx-e150d0.exe (current)
UPDATE: It looks like Dr. Thomas now publishes the Windows version along with the Mac version on the GPX's Thing page: http://www.thingiverse.com/thing:81425/#files