What is the correct reading for the word 士 in the context of this phrase, "有能の士". I found online that 士 can have both the 音読み reading of し and the 訓読み reading of さむらい. However, as 士 is a word that is not usually used alone, I am unable to discern as to which reading is the correct one.
The quick answer is: ゆうのうのし.
The long-winded answer as to how I checked and confirmed this personally is as follows:
I used a monolingual kanji dictionary (Whatever you 'found online' was apparently insufficient). This indicated that while the 音読み is シ as you are aware, the 訓読み is shown as ［外］さむらい or △さむらい. The［外］or △ indicating that this is a non-standard reading.
Now that we know it is a non-standard reading, but we're still not 100%, let's look for similar examples.
From typing "の士" into ALC and looking through the results we get 博雅の士 同好の士 有能の士 独学の士 高潔の士. From Weblio J/E dictionary we get 同好の士 from typing in 士. Now we have 5 examples of this pattern and should expect this character to be read the same in each. Now we want to see if any of these expressions have sufficient reference online to reliably indicate the reading.
It's easy to accidentally skew your results with a little confirmation bias, so try to use your searches to minimize that possibility. For example, upon a search for "どうこうのし" I discovered the hatena.ne.jp link found previously as well as a few others. Nothing, however, appeared for a search of "どうこうのさむらい".