I think that the best way is to write an external DLL (mex file), that
will be called in Matlab environment.
Try a search with google for some examples.
MatLab 6.x has an Instument Control Tool box that lets you
control GPIB instruments and The serial ports. I think the
command is ser(x,x). And if it's not in the Instument
Control Tool box there might be a DAQ tool box.
And try there web site Support page.
Hope this helps.