I believe this can be translated into a question about fractional Helly number, which is answered in a paper of Matousek.
The citation is: Bounded VC-Dimension Implies a Fractional Helly Theorem, Discrete & Computational Geometry, Volume 31, Number 2.
A pdf can be found by googling "the (p,k) property, VC dimension"
For a set $X$, any $\mathcal{F} \subseteq \mathcal{P}(X)$ is a set system on $X$.
Theorem 4 of the paper states:
Let $\mathcal{F}$ be a set system with $\pi_{\mathcal{F}}^*(m) = o(m^k)$ for some integer $k$, and let $p \geq k$. Then there is a constant $N$ such that the following holds for every finite $\mathcal{G} \subseteq \mathcal{F}$: If $\mathcal{G}$ has the $(p,k)$ property then $\tau(\mathcal{G}) \leq > N$
The terminology in the theorem can be found online, but I will list some definitions here.
The symbol $\pi_{\mathcal{F}}^*(m)$ refers to the dual-shatter function of $\mathcal{F}$.
A sufficient condition for the assumption $\pi_{\mathcal{F}}^*(m) = o(m^k)$ is simply that the independence dimension of $\mathcal{F}$ is at most $k-1$. If you are unfamiliar with the dual-shatter function, more can be found in this paper: http://arxiv.org/abs/1109.5438.
We say that $\mathcal{F}$ has the $(p,k)$-property if among any $p$ elements of $\mathcal{F}$, some $k$ have non-empty intersection.
The transversal number of $\mathcal{F}$, denoted $\tau(\mathcal{F})$, is the least integer $N$ such that there is a subset $X_0 \subseteq X$ with $|X_0|=N$, and $F \cap X_0 \neq \emptyset$ for every $F \in \mathcal{F}$.
YourI will try to translate your question can be translated as follows. We make the assumption that there is some theory $T$ and monster $M \models T$ with respect to which formulas are evaluated.
Let $\varphi(x,y)$ be the given formula. As you remark, if $x$ and $y$ are tuples, rather than arity 1, it makes no difference. For sets $A$ and $B$, let $S_\phi(B)^A$ denote the set family
$$\lbrace \varphi(a;B): a \in A \rbrace$$
Take $\mathcal{F} = S_\phi(M)^M$. Since $T$ is NIP (note we need only $\varphi$ NIP), $\mathcal{F}$ has finite independence dimension, say $d$. If $d=0$ then $\mathcal{F}$ is finite, and the claim follows. Assume $d>0$.
The $k$ that suffices for your claim is $d-1$$d+1$. The $N$ that suffices is given by applying Theorem 4 with $p=k=d-1$$p=k=d+1$.
I will argue for the correctness of this statement. If finite sets $A$ and $B$ are given, your hypothesis allows us to assume that $\mathcal{G} = S_\varphi(B)^A$ has the $(k,k)$ property.
I now need to make an assumption which I cannot really justify, which is that although $\mathcal{G} \subseteq \mathcal{F}\vert_B$ rather than $\mathcal{G} \subseteq \mathcal{F}$, this makes no difference.
Given this assumption, Theorem 4 now gives a $B_0 \subseteq B$ of cardinality $N$ which pierces $\mathcal{G}$. Translating this back to model theory, it is easy to see that $B_0$ is the set sought after.