Do taxis run regularly from the train station in San Giminiano to hotels on Sundays?
There is no train station in San Gimignano
The closest would be Poggibonsi
In a triumph of creative marketing, that train station is called "Poggibonsi-San Gimignano".
I have no idea whether taxis wait for all incoming trains there.
Stay on the safe side and reserve a taxi or other form of transportation in advance; do not assume taxis will be waiting in front of railway stations mainly used by commuters. Or check if any bus is running at the time you need. In any case, San Giminiano is about fifteen minutes driving from Poggibonsi station.
As an alternative it looks like Autonlinee Toscano route 130 SIENA-POGGIBONSI-S.GIMIGNANO- STRADA runs that way at about 20-30 minutes.
Check the schedule here:
https://rd-sftp-data.s3.eu-west-1.amazonaws.com/autolineeToscane/IVU/OUTPUT/TIMETABLES_WINTER/EXSI/130.pdf
Be sure you're checking the Sunday/Festivo/Domenica schedule. Porta San Giovanni should be fine that's just the gate outside the city itself.
Good travels,
=Tod
Checking Google I don't see a set taxi stand outside the train station so it might be that you need to arrange for one to meet you.
Here's a taxi company that offers tours and drives as well as taxi service that seems like they would be willing to take you to SG.
They have an office not far from the train station in Poggibonsi and take reservations.
http://www.taxivaldelsa.it/en/home-2/index.html
Not a recommendation - just another possibility.
=Tod
There is a Taxi stand at the station (as you exit the station building to the right), however there is no guarantee there will be taxicabs waiting outside (on Sunday or any day of the week).
Take a bus or book something with the local private drive service suggested above.
My recollection is San Gimignano is a pedestrian zone within the city walls. So, it depends on the location of your lodging as to whether a taxi can get you to the door.