You need to reach Thrissur, which is prominent station in Kerala. I wouldn't to be able to suggest best route, as I have not travelled from Chennai.
Cochin International Airport is 32 km from Kodungallur, if you travel by air.
Thrissur (37kms) and Aluva (27kms) are the nearest Railway Stations.
Kodungallur is upon NH 66, 35kms north of the city of Cochin and 50 kms south of Guruvayur, The Temple Town.
I am from Malaysia and I can guide you. Take a train to Ennakulam and from there a bus or taxi to the mosque in Kodangallur or stop at Irunchalakuda station and board a bus.
When I visited Kerala, this special mosque was one of my must visit place. My Husband and I had hired a personal driver & car to move us around in Kerala. But I would confidently suggest you to reach Ernakulam, first, and easily get a taxi or cab from there to visit the Cheraman Juma Mosque.
Get quick answers from Cheraman Juma Masjid Mosque staff and past visitors.