Firstly this problem is not well-defined as stated. Let $f(x)=e^{-100x}$ and let $r=f(0)=1$. Since, $\int_0^{\infty}f(x)dx=\frac{1}{100}<1$ there is no $y$ that solves your problem. I am suspecting that you have $f$ so you should convince yourself that the problem actually has a solution.
I always solve this sort of problem by root finding:
Let $H(y)=\int_0^y f(x)dx-r$ then the problem becomes finding a root of $H$. Now there are lots of software packages to solve this, these will give you much better accuracy than trial and error.
In Matlab, the function fzero(fun,x0) will solve this problem.
