At the Guarulhos airport, you should take the bus which is called Airport Bus Service
This bus has several different lines, going to different places. If you want to go directly to the IFT, take the line to Terminal Rodoviário Barra Funda (via Tietê).
You have to first buy tickets at the ticket office, which is located near the entrance to the terminal. It is about 40 reais. You have to buy tickets to Terminal Rodoviário Barra Funda.
There are several bus stops right in front of the terminal, all the same Airport Bus Service. You have to locate the one which goes to Barra Funda (via Terminal Tietê).
The schedule is available on the website:
When I last time looked (in October 2013) it was like this:
06:20 07:00 07:55 09:05
09:55 10:45 11:55 12:45
13:35 14:35 15:35 16:25
17:15 18:05 19:05 20:05
20:55 21:45 22:40
Depending on traffic, the trip will take between 30 and 60 minutes. The final stop is the Barra Funda bus station. It is rather big. Walk up the steps into the upper level of the bus station, turn left and walk until the end of the station. Just follow the sign to Av. Marquês de São Vicente. You are now on the northern side of the station.
If you see this beautiful modern building:
WRONG building! this means that you are on the wrong side of the station. Our institute is on the other side
At the northern side of the station, descend the steps and you will find yourself on a small unnamed street with many city bus stops. On the other side of that street, you will see a large white and blue building. The white and blue building is the Instituto de Artes, and next to the right of it is another (slightly smaller) building which is the Instituto de Física Teórica:
THIS is our institute! You will find the secretaries on the fourth floor.