Are there any recent 64-bit VFW screen capture codecs out there?
You don't need a 64bit codec to use it in 64bit Software like VirtualDub or After Effects, a 32bit codec will work just fine.
For intermediate codecs I generally use either a QuickTime with PhotoJPEG compression or Animation like you suggested yourself. The latter is lossless and produces fairly big files, the former is lossy just like JPEG but offers visually lossless compression with a reasonable size and works very well in every software that supports QuickTime video.

Another alternative would be a JPEG2000 image sequence which can be be either lossless or lossy, though its a bit less fun to work with as you end up with thousands of files in a folder, though there are commercial JPEG2000 codecs out there that are 64bit native and integrate into Windows.

Another good (open source) alternative is Ut Video. It also features a native 64bit version of the codec and integrates into Windows aswell. It's completely lossless but produces files with reasonable size.