You can take the fast ferry from Istanbul to Bandırma, which would take around 1 hour 45 minutes. There's also fast ferry from Yenikapi ( the port in Istanbul) to Bandırma. For further information on the boat schedules you can contact IDO (Istanbul Sea Buses Company).
There are ferryboats running between Çanakkale-Eceabat, Çanakkale-Kilitbair, Gelibolu-Lapseki, Bozcaada-Odunluk, Çanakkale-Gökçeada and Kabatepe-Gökçeada. The Çanakkale Port Authority Phone numbers are;
Eceabat Port : (+90 286) 814 1033.
Gelibolu Port : (+90 286) 556 1617.