Ft. Kochi (Ft. Cochin) has some well-preserved architecture, and is a pleasant place to walk around. It certainly gets backpackers, but it also has higher-end hotels. Definitely appeals more to foreigners than Indians.

I've stayed at the Old Habour hotel, which is cute but not totally sealed so mosquitoes get in. I also stayed in the Malabar House, which is a little pricier, but a much more modern hotel. Their restaurant (Malabar Junction) is fairly innovative, and serves up lovely seafood dishes. For dessert, try the chocolate samosas.

Houseboats are tranquil, but not that interesting IMO.

The Karela Tourism authority puts on a good day-long boat tour (including lunch). It's definitely aimed at the backpacker crowd, but if you're interested in the agriculture/industries of the reason, it's a good way to see them.