Is there a feminine equivalent to aruji? If a servant was addressing a noblewoman, what term would they use? I am looking for the more archaic term, not one that would used in current ordinary speech. (I understand that 'aruji' is fairly archaic.)
First, 主【あるじ】 is not particularly gender-specific, but it's not a very common way of addressing one's master, either. It sounds relatively blunt and less sophisticated. If you want to play it safe, avoid aruji altogether. (It can be natural in some fictional situations, though. For example, one user of aruji I know is a young and proud beast girl who is basically loyal to her master but is not good at keigo and treats him like her friend. Other possible users of aruji would be a bandit, a samurai living in the countryside, a dwarf living in a remote cave, etc.)
The common words used by classic housemaid/butler/servant type characters are ご主人様 for a male owner, 奥様 for a married woman, and お嬢様 for an unmarried lady. ご主人様 and お嬢様 are something you would hear at "maid cafés" in Japan.