“I hear lots of complaints about how the scientific method is flawed because of it's reliance on methodological naturalism, but nobody who complains about seems to be able to say exactly what it should be changed to or replaced with. They just complain about it.”
A naturalistic methodology (sometimes called an "inductive theory of science") has its value, no doubt. […] I reject the naturalistic view: It is uncritical. Its upholders fail to notice that whenever they believe to have discovered a fact, they have only proposed a convention. Hence the convention is liable to turn into a dogma. This criticism of the naturalistic view applies not only to its criterion of meaning, but also to its idea of science, and consequently to its idea of empirical method.
– Karl R. Popper, The Logic of Scientific Discovery
It's better than nothing, which so far is the alternative.