We stayed in Le Meridien in Cochin, 30min away from Fort Cochin ( centre ) but great bar, pool, spacious rooms etc. Hire a local and he will drive you around throughout your stay, they're cheep and very reliable!
Old Harbour Hotel is beautiful colonial small hotel within the old Fort Cochin ( Old Town), if that's what you're looking for check it out as it was fully booked last time we had a look!
Have fun, aaaand pls don't miss 'Back Waters' tour! We loved it, kids will ask you for pencils when you go, we where not told last time we went and felt terrible !!!
Check out Tripadvisor Kochi
http://www.tripadvisor.com/Hotels-g297633-Kochi_Kerala-Hotels.html
Of the hotels mentioned, I would recommend Old Harbour Hotel, Malabar House and the Brunton Boatyard for places with some history. There is another hotel called the Koder House, right next to Old Harbour, which is a historical building that has housed dignitaries.
For location, can't beat Old Harbour and Koder house. No beach but right opposite the sea and the chinese fishing nets. Brunton is a luxury chain hotel that sits at the harbour mouth. You can watch as the tankers and container ships glide past slowly. All of these are close together with Brunton having the best sea view.A couple of minutes walk gets you to Princess Street and lots of small cafes and shops around. Try the Kashi Art cafe for some local artists and good food.
Another place that I would recommend, if only for its location, is the Poovath Heritage Hotel. It's a recently refurbished family home that is right on the beach and next to the Dutch cemetary. This alongwith Malabar House hotel, mentioned above, are right in the sightseeing zone. Malabar House is on a lane opposite the parade grounds.
I've not stayed at any of these hotels but have visited/dined at Old Harbour, Malabar House and Brunton Boatyard and can vouch that they are clean, beautiful and have lovely service. Fort Kochi is beautiful. Hope you have fun.