Let $G$ be a nilpotent closed subgroup of the group $UT(n,\mathbb{R})$ of upper triangular matrices with $1$-s on the diagonal.
I can construct a Lie algebra from $G$ in two ways:
The usual Lie algebra of a matrix Lie group consisting of matrices $A\in M_n(\mathbb{R})$ for which $\exp(tA) \in G$.
I can take the lower central series of $G$, take a direct sum of the factors and define Lie brackets in the natural (grading respecting) way.
Are the two Lie Algebras isomorphic? If so, canonically? (I'm new to this business)
No. If the Lie algebra (i.e. the first construction) is denoted $\mathfrak{g}$, then the second one will be isomorphic to the associated Carnot-graded Lie algebra $\mathrm{Car}(\mathfrak{g})$.
Since there exist finite-dimensional nilpotent real Lie algebras (in dimension $\ge 5$) $\mathfrak{g}$ that are not isomorphic to their associated Carnot-graded Lie algebra, and since any finite-dimensional nilpotent real Lie algebra is isomorphic to a subalgebra of $\mathfrak{ut}(n,\mathbf{R})$ for some $n$, you get a negative answer to your question (at least for $n$ large enough, probably for all $n\ge 4$ actually).