We never used the "temporal" thermometers others recommend so I'm not familiar with them. If they are the little bands that you stick to a kid's forehead -- we tried those and they were lousy and only gave you a general indication and not an actual temp in readable degrees. But maybe they're better now?
Our pediatrician has written articles for journals about fever in children, so I tend to take her word as the best advice. I always took my daughter's temps rectally -- the doc said that was the only truly accurate way to do it in young children up to the age when they can hold one in their mouths reliably. Under the arm is not a good place -- one wiggle and the kid has exposed the thermometer to the air, skewing the reading.
Any decent digital thermometer will do. You need to get some KY Jelly and plenty of thermometer covers, and I also recommend you get alcohol swabs (the first aid kit kind) to clean the thermometer (even though I also used a cover every time, I always swabbed it afterward once the cover was in the trash). If you're really worried about the rectal area and possibly contaminating your hands, keep disposable gloves around.
It does not hurt the child, though it may surprise him the first few times and he may cry at the different sensation until he realizes it does not hurt him. But because he has febrile seizures, you need to stop merely guessing at his temperature and giving him medications on a wing and a prayer. You need data. Let him watch TV while you do it, whatever it takes to get him distracted. Digital thermometers are fast; get the fastest one available, write "rectal only" on it with a Sharpie and get yourself used to using it.
I'm pretty amazed your doctor hasn't told you to get one of these new temportal thermometers if they're good or to do rectal temps since your so is prone to febrile seizures. Or that your doc hasn't told you to get some very expensive but good ear thermometer like the docs use -- the ones from the drugstore are useless!!. I have heard many times that the ear temps are also not very accurate and most parents can't get the kind of very advanced ear thermometer that doctors use, but if you can get one of those, go for it instead. But please stop guessing and risking your son's health.