I had a question about the number people practicing Islam in parts of New York for a question about the dietary practice known as halal. I used The ARDA search mechanism and found files describing the number of Muslims by county.
Other sources of religious data: Hartford Institute for Religion Research and Glenmary Research - the latter especially good for a breakdown of Roman Catholic numbers.
Not so incidentally, it would be a mistake to assume that most U.S. Arabs are Muslims. In fact, if you go here, you'll see that most Arab-Americans are Christians.