I'm sure there is a much better way to do this. Anyway here is my Claim:
Let $M^m\subset\mathbb R^{m+n}$ be an embedded $C^1$ manifold with $C^1$ boundary, and let $\omega\in\Omega^{m-1}(M)$ be $C^1$ with compact support, then $$\int_M d\omega=\int_{\partial M}\omega $$
Here, as usual, a $C^1$ manifold with $C^1$ boundary is defined to be a subset that is locally the image of $\mathbb R^m$ the upper half space $\mathbb H^m\subset \mathbb R^m$ under a $C^1$-embedding $\phi:\mathbb R^m\to \mathbb R^{m+n}$. And a $C^1$ form $\omega\in\Omega^k(M)$ is just the restriction of a $C^1$ form in $\Omega^{k}(\mathbb R^{m+n})$ to $M$. And we define the integral of a continuous, compactly supported form $\eta\in\Omega^m(\mathbb R^{m+n})$ over $M=\phi(\mathbb H^m)$ to be
$$\int_M \eta =\int_{\mathbb H^m}\phi^*\eta,$$
and we use ($C^1$) partitions of unity to define $\int_M \eta$ over manifolds with more than one chart. Here, $\phi^*\eta$ is defined as usual by
$$\phi^*\eta(v_1,\cdots,v_m)=\eta(d\phi(v_1),\cdots,d\phi(v_{m+n}))$$
(i.e. here we consider $\phi$ not as a smooth map from $\mathbb H^m$ to $M$, but from $\mathbb H^m$ to $\mathbb R^{m+n}$). The theorem then follows if we can prove that
$$\int_{\partial\mathbb H^m}\phi^*\omega=\int_{\mathbb H^m}\phi^*(d\omega).$$
Unfortunately, the forms we are integrating on the left and right hand side are both generally only continuous. And applying the fundamental theorem of calculus requires that the form on the left be continuously differentiable.
My argument consists of splitting the form into pieces, and constructing charts for each piece such that the form on the left becomes differentiable, and applying Stokes' theorem on each piece.
Step 0
I start by quickly showing why this the claim is true when $n=0$. In this case we can find an open cover consisting of cubes (products of open intervals, $U_i=(a^{(1)}_i,b^{(1)}_i)\times\cdots\times(a^{(m)}_i,b^{(m)}_i)$ ) $U_i\subset \mathbb R^n$ such that $U_i$ is (1) either entirely contained in the interior of $M$, or (2) that we have (up to reordering of coordinates) $$U_i\cap M=\{x\in U_i:x_m\leq q(x_1,\cdots,x_{m-1})\}$$ or (3) $$U_i\cap M=\{x\in U_i:x_m\geq q(x_1,\cdots,x_{m-1})\}$$ for some $C^1$ function $$q:(a^{(1)}_i,b^{(1)}_i)\times\cdots\times(a^{(m-1)}_i,b^{(m-1)}_i)\to(a^{(m)}_i,b^{(m)}_i).$$ Now we may use a partition of unity to reduce to the case that $\omega$ is supported in one of these cubes. Let's say that we're in the case (2). Then write $\omega=\sum_ia_idx_1\wedge\cdots\wedge \widehat{dx_i}\wedge\cdots\wedge dx_m$ we get that $$\int_{U_i}d\omega=\int_{a^{(1)}_i}^{b^{(1)}_i}\cdots\int_{a^{(m-1)}_i}^{b^{(m-1)}_i}\int_{a^{(m)}_i}^{q(x_1,\cdots,x_{m-1})}\sum_i\frac{\partial a_i}{\partial x_i} dx_{m}\cdots dx_1.$$ Taking out the sum and applying the fundamental theorem of calculus to each $\int \frac{\partial a_i}{\partial x_i}dx_i$, we get $$=\int_{a^{(1)}_i}^{b^{(1)}_i}\cdots\int_{a^{(m-1)}_i}^{b^{(m-1)}_i}a_m(x_1,\cdots,x_{m-1},{q(x_1,\cdots,x_{m-1})})dx_{m-1}\cdots dx_1$$ $$=\int_{\partial U_i}\omega.$$And so we're done. (I'm assuming that the reader has seen the proof of the ordinary Stokes' theorem before)
Step 1
Let $A:\mathbb R^{m+n}\to\mathbb R^{m+n}$ be linear and nonsingular, then let $A(M)$ be the image of $M$ under $A$. Then $A(M)$ is still a $C^1$-manifold, and for every continuous $(m-1)$-form $\eta$ we have $$\int_{A(M)}(A^{-1})^*\eta=\int_{M}\eta.$$ Now for every $x\in M$, let $U_x\subset M$ be a neighbourhood of $x$ and $A_x:\mathbb R^{n+m}\to\mathbb R^{n+m}$ be linear such that every projection of $A_x(U_x)$ onto a subspace of $\mathbb R^{n+m}$ spanned by any $m$ of the $n+m$ standard basis vectors is a diffeomorphism onto its image. This is doable using inverse function theorems, a bit of linear algebra ...
We may choose finitely many $U_1,\cdots,U_N$ of these $U_x$, such that the support of $\omega$ is in the union of the $U_i$. If $\rho_i$ is a subordinate partition of unity, then we have that $$\int_M d\omega=\sum_i\int_{A_i(U_i)} (A_i^{-1})^*(d\rho_i\omega)$$and $$\int_{\partial M} \omega=\sum_i\int_{A_i(\partial U_i)} (A_i^{-1})^*(\rho_i\omega)=\sum_i\int_{\partial A_i(U_i)} (A_i^{-1})^*(\rho_i\omega).$$
So we may assume that $M=A_i(U_i)$ for some $i$ and write $\omega$ instead of $\rho_i\omega$.
Step 2
Write$$\omega=\sum_I a_Idx_I,$$where $I$ ranges over tuples $I=(i_1<\cdots <i_{m-1})$, and $a_I$ is a $C^1$ function $\mathbb R^{n+m}\to\mathbb R$. We have$$\int_{\partial M}\omega=\sum_I\int_{\partial M}a_Idx_I.$$We will show that for each $I$ we have $\int_{\partial M}a_Idx_I=\int_{M}d(a_Idx_I)$. Hence may assume that $\omega=adx_1\wedge\cdots\wedge dx_{m-1}$, and so we get $$d\omega=\sum_{j>m-1}\frac{\partial a}{\partial x_j}dx_j\wedge dx_1\wedge\cdots\wedge dx_{m-1}.$$Now because of the work we did in step 2, the projection $\pi(x_1,\cdots,x_{n+m})=(x_1,\cdots,x_m)$ is a diffeomorphism onto its image. Equivalently, $M$ is given the graph $$\Phi(x)=(x,\phi(x)),\phi=(\phi_{m+1},\cdots,\phi_{m+n}),x\in U$$of some $\phi:\mathbb R^m\supset U\to\mathbb R^n$, for some $U\subset\mathbb R^m$ which is a $C^1$ manifold with $C^1$ boundary. We also have that $\partial M$ is the diffeomorphic image of $\Phi|_{\partial U}$.
Step 3
We have that $$\int_{\partial M}\omega=\int_{\partial U}\Phi^*\omega,$$$$\int_{M}d\omega=\int_{U}\Phi^*d\omega.$$And some calculus of forms shows that $$\Phi^*dx_i=dx_i$$ if $i\leq m$, and $$\Phi^*dx_i=\sum_{1\leq j\leq m}\frac{\partial \phi_i}{\partial x_j}dx_j$$ if $i>m$. So we get $$\Phi^*\omega=a\circ\Phi\cdot\Phi^*(dx_1)\wedge\cdots\wedge\Phi^*(dx_{m-1})$$ $$=a\circ\Phi\cdot dx_1\wedge\cdots\wedge dx_{m-1}$$ and this is a $C^1$-form! We also have$$\Phi^*d\omega=\sum_{i>m-1}\frac{\partial a}{\partial x_i}\circ\Phi\cdot \Phi^*dx_i\wedge \Phi^*dx_1\wedge\cdots\wedge \Phi^*dx_{m-1}$$ $$=\frac{\partial a}{\partial x_m}dx_m\wedge dx_1\wedge\cdots\wedge dx_{m-1}+\sum_{i>m}\frac{\partial a}{\partial x_i}\circ\Phi\cdot \frac{\partial \phi_i}{\partial x_m}dx_m\wedge dx_1\wedge\cdots\wedge dx_{m-1}$$And we see that $d\Phi^*\omega=\Phi^*d\omega$. So we've reduced the claim to showing that $$\int_{\partial U}\Phi^*\omega=\int_{U}d\Phi^*\omega,$$ for a $C^1$-form $\Phi^*\omega$, so we have reduced the claim to the case where the codimension $n=0$: As this follows from Step 0, we're done.