Should I ask for a submitted recommendation letter to be retracted in order to submit another, stronger recommendation? I am currently applying for a Ph.D. in Physics in the US. One of my recommenders has already submitted a letter to the schools I'm applying to, but I was advised by another faculty member that I should have gotten a letter from a different professor I worked with since the submitted one wouldn't be as strong. The latter professor would most likely write a stronger recommendation.

All of the programs I'm applying for require three letters, and most allow for four; would simply adding the extra recommender be sufficient or should I contact the school to remove the weaker letter entirely if possible? In other words, would having it there bring down my application if there is a stronger one I could replace it with or would it reasonable to assume that reviewers would consider all four and think of the weaker one as extraneous (since I cannot define a ranked order)?
You can't "retract" a letter.  This isn't done, and I think it would look weird and somewhat suspicious.  The committee might be inclined to read that letter more closely in case it contains something damaging that you were trying to conceal.  At the very least, it seems distasteful to be "gaming" your professors' supposedly well-considered evaluations in this way.

You certainly can have this other professor submit their letter in addition to the others.  For those schools that specify three letters, it will be up to the committee whether they read all four, or choose three in some arbitrary way.  I suspect that if three letters suggest you're a viable candidate, the committee will be willing to look at the fourth.