There's two notions of equivalent polynomials floating around, one saying that $f = g$ iff they're equivalent as maps, and the other saying $f = g$ iff they're equal on each coefficient when written in standard form.
I'm interested in polynomials over a finite field, irreducible polynomials and factoring so what type of equivalence should I use? For instance if we take map equivalence, then there are only a finite number of polynomials. And that makes a huge difference!
Please explain when it's okay to use what.
In my experience, in algebra, equality of polynomials is always equality of their coefficients.
When authors care only about functions induced by polynomials, they usually explicitly state that, or use term like "polynomial function".
One possible place when confusion could have arised (but it doesn't) is when you talk about regular functions defined on algebraic varieties. In classical algebraic geometry, these were just functions defined by polynomials, so in theory it could have happened that two different polynomials result in the same regular function on the affine space. The solution is that classical algebraic geometry always works with algebraically closed field as a base field, which must be infinite.
To be able to talk about varieties defined over non algebraically closed fields, one usually uses language of schemes, but regular functions defined on schemes aren't really "functions" anymore, so there's no problem either. Also, morphisms between schemes are also defined so that it's quite obvious that different polynomials (or actually different ring homomorphisms) give different morphisms, even if they're equal on point-set level.