I want to calculate the (simplicial) homology of the following space using Mayer-Vietoris:
I have tried to do it by cutting it along the axis and getting two subspaces homeomorphic to something that looks like an "infinite flute" (a cylinder with infinitely many holes in its surface) such that the intersection is homeomorphic to the 1-dimensional sphere.
But doing this I still have to calculate the homology of the "infinite flute"
Is this the right choice for the subspaces? Or are there any other subspaces which would make the calculations easier?

Here's a Mayer-Vietoris argument. Write $X$ as a union $\cup_{i=0}^\infty T_i$ where each $T_i$ is a torus with two boundary components (except $T_0$, which has only one boundary component). Let $A= \sqcup_{i=0}^\infty T_{2i}$ and $B= \sqcup_{i=0}^\infty T_{2i+1}$. Then $A \cap B$ is a countably infinite disjoint union of circles $\sqcup_{i=1}^\infty S^1_i$. Mayer-Vietoris gives you a long exact sequence containing the following terms: $$0 \to H_2(A) \oplus H_2(B) \to H_2(X) \to \oplus_{i=1}^\infty H_1(S^1_i) \to H_1(A) \oplus H_1(B) \to H_1(X) \to 0.$$
There might be a way to show that $H_2(X)$ vanishes by analyzing the connecting homomorphism. But there's a better approach that mirrors part of Najib Idrissi's answer: Any nonvanishing class in $H_2(X)$ is represented by some cycle $\sigma \in C_2(X)$. Since $\sigma=c_1\sigma_1+ \cdots +c_k \sigma_k$ is a finite linear combination of compact simplices, there is some punctured genus-$g$ surface $\Sigma_g \subset X$ which contains all the simplices $\sigma_1,\ldots,\sigma_k$. So $\sigma \in C_2(X)$ is in the image of the inclusion map $C_2(\Sigma_g) \hookrightarrow C_2(X)$, and thus $[\sigma]\in H_2(X)$ is in the image of the inclusion-induced map $H_2(\Sigma_g) \to H_2(X)$. But it's a standard fact that a punctured compact surface $\Sigma_g$ has $H_2(\Sigma_g)=0$, so $[\sigma] \in H_2(X)$ must equal zero. We conclude that $H_2(X)=0$.
Now the above reduces to a short exact sequence $$0 \to \oplus_{i=1}^\infty H_1(S^1_i) \to H_1(A) \oplus H_1(B) \to H_1(X) \to 0.$$ We have $$H_1(A) \oplus H_1(B) \cong \oplus_{i=1}^\infty H_1(T_i),$$ where $H_1(T_0)\cong \mathbb{Z}^2$ and $H_1(T_i)\cong \mathbb{Z}^3$ for $i\geq 1$. We can view the "third" generator of each $H_1(T_i)$ for $i\geq 1$ as the image of the generator of $H_1(S^1_i)$. This gives $$H_1(X) \cong \frac{H_1(A)\oplus H_1(B)}{\oplus_{i=1}^\infty H_1(S^1_i)}\cong \oplus_{i=0}^\infty \mathbb{Z}^2.$$ Finally, connectedness gives $H_0(X)\cong \mathbb{Z}$. In summary, we have $$H_*(X) \cong \begin{cases} \mathbb{Z} & *=0\\ \oplus_{i=0}^\infty \mathbb{Z} & *=1 \\ 0 & *\geq 2.\end{cases}$$