Did you buy your sightglass or make it yourself? Typically the tubing you want is clear polypropylene. You can find this at omega.com or mcmaster.com. If you bought a pre-made one, it should be made with this material already.
I have the same issue whenever I use my HLT as a brew kettle, for it has a clear polypropylene sightglass tube connected to a brass compression elbow. What happens, in my setup, is the heat from my burner actually boils the liquid in the sightglass well before the actual kettle boils. Thus, the wort boils and bubbles up through the tube. Since my sightglass is open to the air (i.e. it does not return to the top of the kettle), I just put a piece of teflon tape on the top during the boil. Watch out: if you remove this before the kettle is cool, liquid will shoot out of the tube like a geyser.
Therefore, you probably are not sucking in air, but are just boiling off what's in your sightglass.