What kind of mobile phase additives are you using? Often a low concentration (up to a few mmol) of either ammonium acetate, formic acid or acetic acid can help shift the balance away from the sodiated molecule towards the protonated molecule.
In general I would not ever recommend using the sodiated peak for analysis, as the sodium level is from trace residues rather than anything you intentionally put in. Even if the batches you're analyzing are 99.5% pure, traces of common ions like sodium could be part of that 0.5% and it makes a big difference in terms of the ions you ultimately see.
If your mobile phase bottles seem to be contributing to the sodiated peak issue, you may want to try removing those bottles, subjecting them to a nitric acid wash, rinsing back out with DI water, and then try again. My lab also has an ICP-MS - we have a few glass bottles that originally contained concentrated nitric acid and have been washed many times through before turning them into DI water dispensers. I noticed that the water dispensed out of those bottles did not have appreciably higher sodium counts than the water direct from our DI generator.
