You can not re-charge in a small unstaffed stn where only card reader is placed like this photo.
https://pbs.twimg.com/media/DEnhhIcUwAAUc0Z.jpg:large(It is also possible for unmanned stns if there is a ticket vending or re-charge only machine)
However, the benefits of using an IC card(Suica,PASMO and more) are basically two.
First one is that you do not have to bring cash, mainly extra too much coins already you know,
other one is to avoid having to buy paper tickets every time at stn ticket vending machine.
Therefore, although it is certain that it can be re-charged at stn ticket vending machine,
but there is not necessarily a time margin every time
and crowded at the nearest stn of famous sightseeing spots such as Kyoto is usual.
so it is easier to re-charge at convenience store that you find soon.
But this simple reason is the same in Tokyo even in other urban areas,
it is because many people often experience a small lost by finding out
where the entrance to the stn is, especially the subway underground stn, right?
This is re-charge at stn ticket vending machine of Nankai (PiTaPa area),
https://youtu.be/P2BkpY0dcTYbut the lang switching button on the upper right is hard to see with reflection of lights.
https://i.imgur.com/l2n7KyS.jpgThe convenience store that can be charged are these 8 companies,
https://i.imgur.com/0naJg7x.pngbut it is possible to find out immediately only famous big 3, 7-11, FamilyMart, and LAWSON.
Sunkus and Circle K was also a big company nationwide,
but most of the stores were absorbed by FamilyMart in last summer.
Currently there are over 66,000 convenience stores in Japan,
but these three companies manage about 60,000 stores.
Although it may seem surprising, Kyoto is a prefecture whose area is several times larger than Osaka,
but the number of convenience stores is about 1/3 of Osaka,
however, it does not have any problem if it only goes around the famous tourist spot in Kyoto city and around.