There are buses from Istanbul at any time, day or night. Just go to Istanbul's main intercity bus station (otogar), and look for 'Çanakkale' signs on the windowpanes of bus company offices. It takes five and a half to six hours to get from Istanbul to Çanakkale.
Kamil Koç (İstanbul Otogar, Bayrampaşa-Esenler, ☎ 444-0-562 (non-prefixed country-wide except cell-phones from which you should dial +90 212 444-0-562); +90 212 658-20-00 (firstname.lastname@example.org), is one of the bus companies transporting passengers for 50 TL pp between Istanbul and Çanakkale.
Truva Turizm (İstanbul Otogar no: 137, Bayrampaşa-Esenler, ☎ +90 212 658-33-86 (email@example.com, fax: +90 212 658-33-89), covers the same route for 45 TL pp (might be a few liras cheaper if the ticket is bought online through their website, but you will need Turkish language skills for that).
The busy Çanakkale bus station also has several daily connections with most major Turkish destinations, such as Edirne and Izmir.