I am currently trying to determine the location of air ingress by spraying Helium at suspected leak locations and measuring the amount from the Vacuum pump discharge.  Is there a better way of performing this check on locations that are below the water level?

Maybe. During an outage , drain the condenser hotwell, and use an ultrasonic noise generator and sensing microphone. However, this will not pickup leaks that may be caused by cracks that have opened up  due to on line forces, such as weight of condensate or vaccuum forces.

Generally, the only good ways are the following:
1.  Helium/ SF6 gas testing.  In the old days we were able to use Freon - till the greenies complained about the ozone layer.  This method works well, but takes a long time to complete.
2.  Flood testing.  During an outage, fill the condenser with water, and look outside for any leakage.  Just a warning that some condensers are not designed to carry a full volume of water without having supports installed - chek with your OEM.  Also check around your LP heaters and HP heaters if they have a vent to condenser.  Many problems arise from this area.
3.  Ultrasonic leak testing on a power plant to try and find leaks on a vacuum system do not work.  Generally the background noise is just too bad.  
4.  Always try to distinguish between above and below the water line.  Generally leaks below the condenser normal working level is associated with an increase in condensate dissolved oxygen, whereas leaks above the water line is not.  
5.  Never trust your chemist - always have them check their oxygen analyser with a test sample before you cart all the equipment to site.