I don't see any obvious way to switch the input programmatically, though the "Speech" companion guide's first paragraph in the "Recognizing Speech" section seems to imply other inputs can be used. I think this is meant to be set via System Preferences, though. I'm guessing it uses the primary audio input device selected there.
I suspect, though, you're looking for open-ended speech recognition, which NSSpeechRecognizer is not. If you're looking to transform any pre-recorded audio into text (ie, make a transcript of a recording), you're completely out of luck with NSSpeechRecognizer, as you must give it an array of "commands" to listen for.
Theoretically, you could feed it the whole dictionary, but I don't think that would work since you usually have to give it clear, distinct commands. Its performance would suffer, I would guess, if you gave it a bunch of stuff to analyze for (in real time).
Your best bet is to look at third-party open source solutions. There are a few generalized packages out there (none specifically for Cocoa/Objective-C), but this poses another question: What kind of recognition are you looking for? The two main forms of speech recognition ('trained' is more accurate but less flexible for different voices and the recording environment, whereas 'open' is generally much less accurate).
It'd probably be best if you stated exactly what you're trying to accomplish.