I sent the manufacturers of the sensor your question and got this response back:
Thanks for the email. There is no real way to waterproof the EZ0 sensors. Waterproofing must be done at the transducer level for proper performance to be obtained. One customer did have some success with open cell foam. You can view the complete article on our FAQ page. We have not been able to identify the specific foam that worked in this application so we do not have a part number to reference.
Please click this link to view the write-up. http://www.maxbotix.com/MaxSonar-EZ1...sensor_outside
So it would seem you could try the open cell foam. I would think there are other ultrasonic transparent materials available as well, they just have to be selected.