I want to write some code to do acoustic analysis and I'm trying to determine the proper tool(s) for the job. I would normally write something like this in Python using numpy and scipy and possibly Cython for the analysis part. I've discovered that the world of Python audio libraries is a bit chaotic, with scads of very limited packages in various states of development.
I've also come across a bunch of audio/acoustic specific languages like SuperCollider, Faust, etc. that seem to make the audio processing easy but may be limited in terms of IO and analysis capability.
I'm currently working on Linux with Alsa and PulseAudio installed by default. I would prefer not to involve and of the various and sundry other audio packages like Jack if possible, though that is not a hard requirement.
My primary interest in this question is to determine whether there is a domain specific language that will provide for quicker prototyping and testing or whether a general language like Python is more appropriate. Thanks.
I've got a lot of experience with SuperCollider and Python (with and without Numpy). I do a lot of audio analysis, and I'm afraid the answer depends on what you want to do.

If you want to create systems that will input OR output audio in real time, then Python is not a good choice. The audio I/O libraries (as you say) are a bit sketchy. There's also a fundamental issue that Python's garbage collector is not really designed for realtime stuff. You should use a system that is designed from the ground up for realtime. SuperCollider is nice for this, and as caseyanderson notes, some of the standard building-blocks for audio analysis are right there. There are other environments too.
If you want to do hardcore work such as applying various machine learning algorithms, not necessarily in real time (i.e. if you can get away with reading/writing WAV files rather than live audio), then you should use a general-purpose programming language with wide support, and an ecosystem of good libraries for the extra things you want. Using Python with libs such as numpy and scikits-learn works great for this. It's good for quick prototyping, but not only does it lack solid realtime audio, it also has far fewer of the standard audio building-blocks. Those are two important things which hold you back when prototyping audio pipelines.

So, then, you're caught between these two options. Depending on your application you may be able to combine the two by manipulating the audio I/O in a realtime environment, and using OSC messaging or shell scripts to communicate with an external Python process. The limitation there is that you can't really throw masses of data around between the two (you can't sensibly pipe all your audio across to some other process, that'd be silly).
Audio Domain Specific Language vs Python