I'm fairly biased in this matter as I just did an acoustical masters. My school, FAU in south Florida, has multiple professors working in acoustics. Mostly the work is hydroacoustics as the program used to be Ocean Engineering, but within that there's a professor who I think is well ingrained with the ASA, and works clossely with WHOI; one professor does hydroacoustic communications, mostly for the NAVY I think; and my thesis advisor studied at Southampton, and does a lot of flow noise work in conjunction with VT. In addition there are a couple Sonar labs. Our program has always been very geared towards the NAVY as we used to get funding from them.
But its more important to find a program that specializes in the specific area you want to get into, I'd search through JASA to see what comes up that peaks your interest.