Yes, if the beer/water mixture isn't "mixed" well, then your original gravity reading will probably be off. Aeration is a good thing before fermentation starts in the fermenter. After fermentation is complete it is a bad thing. So stirring vigorously, will not only help your yeast, but also help with your hydrometer readings. In the meanwhile (I'm assuming your doing an extract brew), I'd just use the OG that is suggested in the recipe/instructions. Extract brewing is a known efficiency, so your OG should be pretty darn close to the suggested one.