Without loss of generality, assume the larger stack is of size $q$. Here's a non-constructive partial result:
If $q > 2p$, Alice wins.
I'll refer to the player whose turn it is as the "current player".
Let $q=np+r$, where $r$ is the remainder of $\frac{q}{p}$. Since $q>2p$, $n\ge2$. Eventually the game will reach the state $(r,p)$: players will take multiples of $p$ from the stack that is currently of size $q$ until that stack is smaller than $p$. At that point, the size of that stack will be $r$, and the other stack will be $p$, with $r<p$.
Since a tie is not possible, either the current player in the state $(r,p)$ can force a win, or the other player can. Alice can control whether she is the current player in the state $(r,p)$.
If the current player wins at $(r,p)$, Alice should take $(n-1)p$ pancakes from the $q$-stack, making the state $(p,p+r)$. She can always do this, since $n\ge2$. Bob's only move in that state is to take $p$ pancakes from the $p+r$ stack, making the state $(r,p)$ and Alice the current player. Thus, Alice wins.
If the current player loses at $(r,p)$, Alice should take $np$ pancakes from the $q$-stack, making the state $(r,p)$ with Bob the current player. Thus, Bob loses (and Alice wins).
Note that this tells us that Alice can win in the case that $q > 2p$, but it doesn't tell us how. We know there is a move that she can use to put herself in a winning position, but if we were Alice, we wouldn't know from this analysis what that move is.