For all x there exists a y where if x is prime, it is less than or equal to y and y is prime.
$\forall x \exists y\space (prime(x) \implies x \leq y \land prime(y))$
There exists a y for all x where if x is prime, it is less than or equal to y and y is prime.
$\exists y \forall x \space (prime(x) \implies x \leq y \land prime(y))$
Both $x$ and $y$ are natural numbers.
The statement should say "there is a largest prime number". I'm aware that switching quantifier order when quantifiers are mixed should change what's being said, but I don't see any difference in effect between the two statements.
If pressed, I'd say that $y$ in the second refers to one $y$ which is the largest prime, while $y$ in the first refers to multiple $y$s which are larger than any given prime.