Well, I see that I disagree with the other posters here.. but I graduated from nursing school not too long ago and we were told that taking a rectal temperature is not recommended so much because it is invasive, traumatic, and while it does give a core temp, it is not necessarily a more accurate measure of a fever. There is a risk of anal perforation (small, but there) and it can be traumatic to the skin as well as making the baby unhappy. An accurate temp is one that is taken using proper technique. There is a proper temp range for each part of the body used for measuring temperature with a normal temp taken rectally being higher than an armpit.
For instance in L & D we take newborn's temps in the armpit (axillary). We do it this way because it is less invasive and we know the range of normal temp values in the armpit, which is lower than rectal but not WRONG, just different. So I know I am probably not explaining this clearly but if you know that your son's armpit temp is usually 98.5 and one day it is 99.5 you know that he is running a low-grade temp. If you took his rectal temp as well it would be slightly higher because it is a core body temp, but it is not a more accurate way to take the temp... just always slightly higher because it is core body temp.
I would ask your son's doc's office nurses how they take an axillary temp. Learn the technique (it's very easy) and take his temp every day to get it down and understand his baseline. Then you can take a temp if you suspect and issue and know exactly how it stands and how you compare.
Many hospitals use ear thermometers as well and I have heard they are less accurate as well, but they are still commonly used.
Good luck.