ser.read(64) should be ser.read(size=64); ser.read uses keyword arguments, not positional.
Also, you're reading from the port twice; what you probably want to do is this:
i=0
for modem in PortList:
for port in modem:
try:
ser = serial.Serial(port, 9600, timeout=1)
ser.close()
ser.open()
ser.write("ati")
time.sleep(3)
read_val = ser.read(size=64)
print read_val
if read_val is not '':
print port
except serial.SerialException:
continue
i+=1