I graduated with a degree in bioinstrumentation from Syracuse University. I'm not sure if the MS program has a instrumentation focus, but you could check out the research pages there. There's a lot of work in sensory systems, and I'm sure some instrumentation work could be done for Master's work. isr.syr.edu is the institute for sensory research's web site.
SU probably isn't the best dept. in the country, but it's far from the worst, the people are great, and a Master's wouldn't take too too long there.
MP