This is actually somewhat complicated in general, and requires some hypotheses on the space $X$. Namely, $X$ must be completely regular, so if your construction does not use this hypothesis it will not in general give the Stone-Cech compactification. See section 1.34 onward of Russel C. Walker's book "The Stone-Cech Compactification." I believe the ultrafilter construction is initially due to Waldhausen, but Walker's exposition is very readable and I can't find the Waldhausen paper.
The upshot is that in general one wants to consider ultrafilters of zero sets of $X$, rather than ultrafilters of closed sets in general. This is necessary because the closed sets of a non-normal space don't behave nicely--in particular, they aren't separated from one another by continuous real-valued functions. But if you look at the universal property of the Stone-Cech compactification, this is exactly the relevant type of separation, so one needs to look at zero sets instead.
EDIT: In response to Qiaochu's comment, I'm going to make some fuzzy remarks on how much of the topology of a topological space $X$ the category Top sees, as opposed to how much of the topology of $X$ the category of compact Hausdorff spaces sees (call this KHaus). I won't be as formal as possible because I think doing so would risk obfuscating some subtle points--but to point in the direction of a formalization, note that there is a functor $F: Top\to [Top, Sets]$ (where $[-,-]$ denotes the functor category), and a functor $G: Top\to [KHaus, Sets]$ where both functors are given by $X\mapsto \operatorname{Hom}(X, -)$. The question I want to address is---how much of the topology on $X$ can we recover from the functors $F(X), G(X)$?
Now for the first question, Top sees everything about a topological space $X$. This is obvious from the Yoneda lemma, but more explicitly, one can consider the two-point space $A=\{x, y\}$, where the open sets are $\emptyset, \{x\}, \{x, y\}$. Then $\operatorname{Hom}(X, A)$ gives exactly the open/closed sets of $X$, and one can even extract the (closed) sets themselves by taking the pullback of diagrams of the form $X\to A\\leftarrow \{y\}$.
But note that the space $A$ is not contained in KHaus, since $x$ is not a closed point. One should think of KHaus as only seeing "zero sets," or more generally level sets, of functions on $X$. Indeed, given any function $f: X\to Y$ in KHaus, one may extract the level set $f^{-1}(y)$ by taking the pullback of $X\to Y\leftarrow y$ (which may not exist in KHaus, but one can see the functor it represents). On the other hand, if $S$ is a closed subset of $X$ which is not the level set of any function, how do we see it? For example, $\operatorname{Hom}(A, Y)=\operatorname{Hom}(pt, Y)$ for any compact Hausdorff space $Y$---KHaus does not distinguish these two spaces.
The upshot is that KHaus only "sees" zero sets (or more generally, level sets of functions), so any natural functor defined out of KHaus will be built from them, rather than arbitrary closed sets.
EDIT 2: This is an attempt to address Qiaochu's Edit #2. I claim that it suffices to quantify over spaces of cardinality at most that of $X^{\mathbb{N}}$. Indeed, let $C$ be any compact Hausdorff space, and $f: X\to C$ a function. Then it factors through $\overline{f(X)}$ which is closed in $C$ and thus compact Hausdorff, and has cardinality at most $X^\mathbb{N}$. So it suffices to quantify over compact Hausdorff spaces of bounded cardinality.
To see the claim about the cardinality of $\overline{f(X)}$, note that $f(X)$ has cardinality at most that of $X$, and there is a surjective map from convergent sequences in $f(X)$ to $\overline{f(X)}$ (namely taking the limit). But convergent sequences in $f(X)$ are a subset of $f(X)^{\mathbb{N}}$.
Now the class of isomorphism classes of compact Hausdorff spaces of bounded cardinality (or indeed, of topological spaces of bounded cardinality) is clearly a set, which lets the quantification go through.
EDIT 3: Qiaochu points out that I assumed the existence of a locally countable base in the last edit---we can't say that every point is the limit of a sequence; instead one needs to say it's the limit of an ultrafilter. This gives a larger bound on cardinality, but still a bound.
If $(X,\Sigma)$ is a measurable space, I think you are asking for a $\sigma$-algebra structure on $|\Sigma|$, the underlying set of $\Sigma$. We can identify this set with the set of measurable functions
$$|\Sigma|\cong \text{Hom}_{\text{Meas}}\;(X,2),$$
where $2$ is a two-point space with discrete $\sigma$-algebra.
Thus it suffices to prove a more general result: that $\text{Meas}$ is a closed monoidal category. In other words, we would like to know that for any two measurable spaces, $X,Y$, there is a $\sigma$-algebra on the set of maps $\text{Hom}_{\text{Meas}}\;(X,Y)$, which has good formal properties (functoriality, right adjointness to $\otimes$).
The fact that $\text{Meas}$ is a symmetric monoidal closed category was proven by Kirk Sturtz in the paper Categorical Probability Theory. See Section 2.3.
Best Answer
Your set $\partial\mathbb{N}$ is also intensely studied in set theory and known as P(ω)/Fin. What you have done is mod out by the ideal of finite sets. People study more general properties P(X)/I, taking the quotient by many other ideals (or by an arbitrary ideal). P(X)/I is a Boolean algebra, and many forcing arguments can be viewed as forcing with this Boolean algebra. The topological properties are very much used in that forcing context, since the generic filters are exactly those containing elements from every ground model dense set. The finite sets become equivalent to the point [emptyset] in this algebra.
Perhaps Lusin was the first to study P(ω)/Fin seriously, and found the phenomenon of Lusin gaps. A gap in P(ω)/Fin is a cut in the order, where the left side increases and the right side decreases, and everything on the left is below everything on the right, with respect to almost-inclusion. Lusin found gaps of various types, including ones with uncountable cofinality.
A particularly interesting case is P(ω1)/I, where I is the ideal of non-stationary sets, and many set theoretic hypotheses, some engaging with large cardinals, interact with the topological properties of that situation.
A few quick examples: