There is no simple way to do this in API 16 that works across all devices.
You will encounter problems with buffer alignment, color spaces, and the need to use different YUV layouts on different devices.
Consider the buffer alignment issue. On pre-API 18 devices with Qualcomm SOCs, you had to align the CbCr planes at a 2K offset from the start of the buffer. On API 18, all devices use the same layout; this is enforced by CTS tests that were added in Android 4.3.
Even with API 18 you still have to runtime detect whether the encoder wants planar or semi-planar values. (It's probably not relevant for your situation, but none of the YUV formats output by the camera are accepted by MediaCodec.) Note there is no RGB input to MediaCodec.
If portability is not a concern, i.e. you're targeting a specific device, your code will be much simpler.
There are code snippets in the SO pages linked above. The closest "official" example is the buffer-to-buffer / buffer-to-surface tests in EncodeDecodeTest. These are API 18 tests, which means they don't do the "if QC and API16 then change buffer alignment" dance, but they do show how to do the planar vs. semi-planar layout detection. It doesn't include an RGB-to-YUV color converter, but there are examples of such around the web.
On the bright side, the encoder output seems to be just fine on any device and API version.
Converting the raw H.264 stream to a .mp4 file requires a 3rd-party library, since as you noted MediaMuxer is not available. I believe some people have installed ffmpeg as a command-line utility and executed it that way (maybe like this?).
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