Troy is about 30 km south of Çanakkale and most travellers visit as a day trip from there. Çanakkale itself is reached by bus from Istanbul (about 6 hours) or by ferry across the Dardanelles from Kilitbahir on the Gallipoli peninsula.
From Çanakkale: Dolmuş minibuses to Troy run from the small bus station behind the central market, leaving roughly every hour through the day and taking around 35 minutes. The fare is very low. Tell the driver "Truva" or "Troy"; they drop you at the site car park. The last dolmuş back leaves in the early evening — check the time when you arrive.
On a tour: Half-day tours from Çanakkale combine Troy with the Trojan Horse film prop on the city seafront and a local commentary. Full-day Istanbul-based tours combine Troy with Gallipoli (often as a long two-day round trip). Both work well; the dolmuş + audio guide is cheaper and more flexible.
By car: From Çanakkale follow the D-550 south, turning off at signs for Troy/Truva (about 25 km). The site car park is on the village of Tevfikiye, a few minutes' walk from the entrance. Parking is free.
There is one small café at the site and another at the Troy Museum a kilometre south. There is no accommodation at Troy itself; stay in Çanakkale.