This is not an answer. Below "finite" means "finite-dimensional over $k$," so "profinite" means "pro-finite-dimensional" and so forth.
The category of coalgebras is the ind-category of the category of finite coalgebras, and hence its opposite is the pro-category of the category of finite algebras, or in other words the category of profinite algebras. Moreover, the category of finite comodules over a coalgebra is equivalent, as a $k$-linear category with fiber functor, to the category of finite continuous modules over the corresponding profinite algebra, where "continuous" means that the action of the algebra factors through one of its distinguished finite quotients. (Here I am not sure where to insert "left" vs. "right," but it doesn't matter for our purposes.)
If $A$ is an algebra, then the profinite algebra corresponding to its category $\text{Mod}_f(A)$ of finite modules is its profinite completion (which is $\text{End}(U)$ where $U$ is the forgetful functor $\text{Mod}_f(A) \to \text{Vect}$, as suggested by Julian Rosen in the comments). If in the question everything is required to be essentially small and "equivalent" is taken to mean "equivalent as $k$-linear categories with fiber functors," then the question is equivalent to the following:
Is every profinite algebra a profinite completion?
This question is harder than I thought it was, and in particular something I really expected to be a counterexample isn't. Fix $k = \mathbb{F}_2$ and consider
$$B = \prod_{i \in \mathbb{N}} \mathbb{F}_2$$
regarded as the cofiltered limit of the projections $B \to \prod_{i \in S} \mathbb{F}_2$ where $S$ runs over all finite subsets of $\mathbb{N}$. The category of finite continuous $B$-modules is the category of finite $\mathbb{N}$-graded vector spaces over $\mathbb{F}_2$, so this is a somewhat simpler version of Todd's proposal in the comments.
Heuristically, the category of finite $\mathbb{N}$-graded vector spaces is the category of finite modules over the algebra generated by countably many commuting orthogonal idempotents $e_i, i \in \mathbb{N}$ (corresponding to projection onto the $i^{th}$ graded component) satisfying the additional relation
$$\sum_{i \in \mathbb{N}} e_i = 1.$$
The problem, of course, is that it is impossible to state this relation. So one might hope to use some kind of compactness argument to prove that $B$ is not a profinite completion. In addition, $B$ is not its own profinite completion: it admits maps $B \to \mathbb{F}_2$ which don't factor through any of its distinguished finite quotients coming from non-principal ultrafilters on $\mathbb{N}$.
Nevertheless:
$B$ is a profinite completion.
To motivate the construction, suppose $A$ is an algebra whose profinite completion is $B$ and $f : A \to B$ is the natural map. Since $A$ and $\text{im}(f)$ have the same finite quotients, we may assume WLOG that $f$ is injective, or equivalently that $A$ is residually finite. Now, $B$ is a Boolean ring: every element of it is idempotent. Hence $A$ is also a Boolean ring.
Every Boolean ring $A$ is the ring of continuous $\mathbb{F}_2$-valued functions on a profinite space $X$, namely its space of $\mathbb{F}_2$-valued points $\text{Hom}(A, \mathbb{F}_2)$. By hypothesis we know what the finite quotients of $A$ are, and hence we know that
$$\text{Hom}(A, \mathbb{F}_2) \cong \mathbb{N}$$
as a set. Hence $A$ must be the ring of continuous $\mathbb{F}_2$-valued functions on $\mathbb{N}$ where $\mathbb{N}$ has been equipped with a profinite (compact, Hausdorff, totally disconnected) topology, and so to construct $A$ it suffices to construct a profinite topology on $\mathbb{N}$.
But this is straightforward: we can use the topology coming from thinking of $\mathbb{N}$ as the one-point compactification of $\mathbb{N} \setminus \{ 1 \}$. With this topology, $A$ is the subalgebra of $B$ consisting of sequences $a_i \in \mathbb{F}_2$ such that $\lim_{i \to \infty} a_i = a_1$.
This construction shows more generally that every profinite Boolean ring is the profinite completion of some Boolean ring, as follows. The category of profinite Boolean rings is the pro-category of the category of finite Boolean rings, and hence its opposite is the ind-category of the category of finite sets, or in other words the category of sets. The profinite completion functor from Boolean rings to profinite Boolean rings is given on opposite categories by taking the underlying set, and so it suffices to show that every set admits a profinite topology, which the one-point compactification construction accomplishes.
On the other hand, I don't see how to adapt this construction to
$$B' = \prod_{i \in \mathbb{N}} M_i(\mathbb{F}_2)$$
regarded as the cofiltered limit of the obvious finite projections as before. The category of finite continuous $B'$-modules is again the category of finite $\mathbb{N}$-graded vector spaces, but with a different fiber functor.