$$J=\int_{-\infty}^\infty\frac{\cos(\alpha x)}{(x^2+1)(x^2+4)}dx\tag{1}$$
$$\frac{1}{(x^2+1)(x^2+4)}=\frac13\left(\frac1{x^2+1}-\frac1{x^2+4}\right)$$
lets make a general integral:
$$I(\alpha,\beta)=\int_{-\infty}^\infty\frac{\cos(\alpha x)}{x^2+\beta^2}dx$$
this defines your integral as:
$$J=\frac{I(\alpha,1)-I(\alpha,2)}{3}\tag{2}$$
Lets use the Feynman technique:
$$I_\alpha=-\int_{-\infty}^\infty\frac{x\sin(\alpha x)}{x^2+\beta^2}dx=-\int_{-\infty}^\infty\frac{(x^2+\beta^2-\beta^2)\sin(\alpha x)}{x(x^2+\beta^2)}dx$$
$$I_\alpha=-\int_{-\infty}^\infty\frac{\sin(\alpha x)}{x}dx+\beta^2\int_{-\infty}^\infty\frac{\sin(\alpha x)}{x(x^2+\beta^2)}dx$$
now notice that this first integral is just the dirichlet integral so we can say:
$$I_\alpha=-\pi+\beta^2\int_{-\infty}^\infty\frac{\sin(\alpha x)}{x(x^2+\beta^2)}dx$$
now what we are going to do is differentiate wrt $\alpha$ again:
$$I_{\alpha\alpha}=\beta^2\int_{-\infty}^\infty\frac{\cos(\alpha x)}{x^2+\beta^2}dx$$
but notice that this is just the same as saying:
$$\frac{\partial^2}{\partial\alpha^2}I(\alpha,\beta)=\beta^2I(\alpha,\beta)$$
now this is just a pretty common pde which we can set up as the following system:
$$I=I(\alpha,\beta)$$
$$I_{\alpha\alpha}-\beta^2I=0$$
$$I(0,\beta)=\int_{-\infty}^\infty\frac{dx}{x^2+\beta^2}=\frac{\pi}{\beta}$$
$$I_\alpha(0,\beta)=-\pi$$
I get:
$$I(\alpha,\beta)=\frac{\pi}{\beta}e^{-\alpha\beta}$$
and so:
$$J=\frac13\left(\pi e^{-\alpha}-\frac{\pi}{2}e^{-2\alpha}\right)=\frac{\pi(2e^{-\alpha}-e^{-2\alpha)}}{6}$$
So yes the $\pi$ should be there. Just a quick note to add: The equation works for $\beta\in\mathbb{R}^+/\{0\},\alpha\in\mathbb{R}^+$