I see you have added an answer - and Charlie's is (more than) fine too.
Here is another way...
First of all - you have checked this, but for completeness - if we endow a real vector space $V$ of dimension $2n$ with a complex structure (i.e.,view it as a $C=\mathbb R[J]$ module), then we have chosen an orientation. For, suppose $v_1,\cdots, v_n$ and $w_1,\cdots, w_n$ are $C$-bases, and $g $ is the transition matrix ($g$ has entries in $C$, or $g = a + Jb$, with $a$, $b$ real) between the two, with determinant $d\in C$. Then $g,$ viewed as a transformation over the reals, has determinant $\det_{\mathbb R}g =d\bar d$, and hence is positive.
Proof: [Updated in 2025, in response to a very valid comment below.]
Viewing $$g\colon V\to V$$ as a $\mathbb R$-linear map, we get a $\mathbb R$-linear map $$\det g\colon \det V \to \det V,$$ where $\det V$ is the real, one-dimensional, vector space $\Lambda^{2n}V$.
Since $\det V$ is one-dimensional, one can identify $\det g$ with a real number once a choice of bases is made: here, we wish to calculate the real number $\mathop{\det} g$ such that
$$w_1\wedge\cdots w_n\wedge Jw_1\wedge Jw_n = {\det} g\, v_1\wedge\cdots v_n\wedge Jv_1\wedge Jv_n.$$ Tensor $V$ with $\mathbb C$ - that is, extend scalars. The determinant 'does not change:'$$({\det}_{\mathbb R}g )\otimes 1 = {\det}_{\mathbb C} (g\otimes 1).$$
Now, $g$ commutes with $J$, so we can calculate $\det_{\mathbb C} (g\otimes 1)$ making use of the fact that $g\otimes 1$ preserves $V_{\pm i}$, the $\pm i$-eigen-spaces of $J$:
For $v\in V$ (or $\in V\otimes{\mathbb C}$), write
$$ v = v^+ + v^-,$$
with $v^{\pm}\in V_{\pm i}.$
[Explicitly, $$v^{\pm} = {1\over 2}\Big(1\pm {J\over i}\Big)v,$$ if one cares.]
Now, $g\otimes 1$, acting on $V_{\pm i}$, is the transition matrix $a\pm ib$ taking $$v_1^{\pm},\cdots, v^{\pm}_n\ \text{to}\ w_1^{\pm},\cdots,w_n^{\pm}.$$ Therefore,
$$w_1^\pm\wedge \cdots \wedge w^\pm_n = \det (a \pm i b) v_1^\pm\wedge \cdots \wedge v^\pm_n,$$
so that
$$w^+_1\wedge\cdots \wedge w^+_n\wedge w^-_1\wedge\cdots \wedge w^-_n = d\bar d v_1^+\wedge\cdots \wedge v_n^+\wedge v_1^-\wedge\cdots v_n^-.$$
Now, the non-zero constant $K$ such that
$$v_1\wedge \cdots\wedge v_n\wedge Jv_1\wedge\cdots\wedge Jv_n= K\, v_1^+\wedge\cdots \wedge v_n^+\wedge v_1^-\wedge\cdots \wedge v_n^-$$ is (of course?) the same that would appear above with the $w_k$ in place of the $v_k$. [Explicitly, $K= (-2i)^n$, if I haven't goofed up.]
Therefore, we also get
$$ w_1\wedge\cdots \wedge w_n \wedge J w_1\wedge\cdots \wedge J w_n = d\bar d\ v_1\wedge\cdots \wedge v_n \wedge J v_1\wedge\cdots \wedge J v_n.$$
The real number $ d\bar d$ is positive, and the above orientation on $V$ does not depend on choice of $C$-basis.
To answer the question proper...
By assumption, $J$ is a global tensor, and thus each $T_p(M)$ is endowed with a $J$ structure, and hence (by the previous argument), an orientation, independent of charts. To bring this in line with the original formulation in your question: suppose
$$\phi: U\subset M\to \mathbb R^{2n},$$ is a chart, and $p\in U$.
Then $\partial/\partial x_1|_p,\cdots ,\partial/ \partial x_{2n}|_p$ - obtained from $\phi$ (or $\phi^{-1}$), is an oriented basis. If the orientation fails to match the $J$ orientation, modify $\phi$ by swapping the first two coordinates. By continuity of $J$, the (modified, if needed) chart will give you an oriented frame on all of $U$ that matches that of $J$. The manifold $M$ is therefore orientable - that is the transition function jacobian determinants will be positive.